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[Refactor] Large scale formatting/linting (#193)

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All html files now prettier formatted and fixes for incompatible blocks applied

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#193
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
This commit is contained in:
Tobias O
2025-11-12 22:47:10 +13:00
committed by jebus
parent 12a20756d6
commit 21d30a923f
114 changed files with 10684 additions and 7009 deletions
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277
templates/objects/composite_rule.html
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@ -2,126 +2,179 @@
{% 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-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
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">
{% 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 %}
<!-- Reaction Patterns -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-reaction-patterns-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-reaction-patterns"
>Reaction Patterns</a
>
</h4>
</div>
<div id="rule-reaction-patterns" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for r in rule.srs %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
<div align="center">
<p>{{ r.as_svg|safe }}</p>
</div>
{% endfor %}
</div>
</div>
<!-- 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 }} <i>({{ s.package.name|safe }})</i></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="rule-aliases-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-aliases">Aliases</a>
<a
id="{{ k|slugify }}_Link"
data-toggle="collapse"
data-parent="#{{ k|slugify }}_Accordion"
href="#{{ k|slugify }}"
>
{{ k }}
</a>
</h4>
</div>
<div id="rule-aliases" class="panel-collapse collapse in">
</div>
<div id="{{ k|slugify }}" 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 %}
{% 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>
{% endif %}
<!-- Reaction Patterns -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-reaction-patterns-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-reaction-patterns">Reaction Patterns</a>
</h4>
</div>
{% endfor %}
</div>
</div>
<div id="rule-reaction-patterns" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for r in rule.srs %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
<div align="center">
<p>
{{r.as_svg|safe}}
</p>
</div>
{% endfor %}
</div>
</div>
<!-- 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 }} <i>({{ s.package.name|safe }})</i></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 %}
{% endif %}
</div>
</div>
</div>
{% endblock content %}

594
templates/objects/compound.html
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@ -2,240 +2,370 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/edit_compound_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/add_structure_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_set_external_reference_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="compound-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ compound.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/compound.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
<p>
The structures stored in this compound can be found at <a target="_blank"
href="{{ compound.url }}/structure"
role="button">Compound structures
&gt;&gt;</a>
</p>
</div>
{% if compound.aliases %}
<!-- Aliases -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-aliases-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-aliases">Aliases</a>
</h4>
</div>
<div id="compound-aliases" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for alias in compound.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Description -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-desc-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-desc">Description</a>
</h4>
</div>
<div id="compound-desc" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ compound.description|safe }}
</div>
</div>
<!-- Image -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-image-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-image">Image Representation</a>
</h4>
</div>
<div id="compound-image" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ compound.default_structure.as_svg|safe }}
</div>
</div>
</div>
<!-- SMILES -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-smiles-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-smiles">SMILES Representation</a>
</h4>
</div>
<div id="compound-smiles" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ compound.default_structure.smiles }}
</div>
</div>
<!-- Canonical SMILES -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-canonical-smiles-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-canonical-smiles">Canonical SMILES Representation</a>
</h4>
</div>
<div id="compound-canonical-smiles" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ compound.default_structure.canonical_smiles }}
</div>
</div>
<!-- InChiKey -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-inchi-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-inchi">InChIKey</a>
</h4>
</div>
<div id="compound-inchi" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ compound.default_structure.inchikey }}
</div>
</div>
<!-- Reactions -->
{% if compound.related_reactions %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-reaction-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-reaction">Reactions</a>
</h4>
</div>
<div id="compound-reaction" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for r in compound.related_reactions %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }} <i>({{ r.package.name|safe }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Pathways -->
{% if compound.related_pathways %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-pathway-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-pathway">Pathways</a>
</h4>
</div>
<div id="compound-pathway" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for r in compound.related_pathways %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }} <i>({{ r.package.name|safe }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Scenarios -->
{% if compound.scenarios.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-scenario-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-scenario">Scenarios</a>
</h4>
</div>
<div id="compound-scenario" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for s in compound.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- External Identifiers -->
{% if compound.get_external_identifiers %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-external-identifier-link" data-toggle="collapse" data-parent="#compound-detail"
href="#compound-external-identifier">External Identifier</a>
</h4>
</div>
<div id="compound-external-identifier" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% if compound.get_pubchem_compound_identifiers %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">
<h4 class="panel-title">
<a id="compound-pubchem-identifier-link" data-toggle="collapse"
data-parent="#compound-external-identifier"
href="#compound-pubchem-identifier">PubChem Compound Identifier</a>
</h4>
</div>
<div id="compound-pubchem-identifier" class="panel-collapse collapse in">
{% for eid in compound.get_pubchem_compound_identifiers %}
<a class="list-group-item"
href="{{ eid.external_url }}">CID{{ eid.identifier_value }}</a>
{% endfor %}
</div>
{% endif %}
{% if compound.get_pubchem_substance_identifiers %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">
<h4 class="panel-title">
<a id="compound-pubchem-identifier-link" data-toggle="collapse"
data-parent="#compound-external-identifier"
href="#compound-pubchem-identifier">PubChem Substance Identifier</a>
</h4>
</div>
<div id="compound-pubchem-identifier" class="panel-collapse collapse in">
{% for eid in compound.get_pubchem_substance_identifiers %}
<a class="list-group-item"
href="{{ eid.external_url }}">SID{{ eid.identifier_value }}</a>
{% endfor %}
</div>
{% endif %}
{% if compound.get_chebi_identifiers %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">
<h4 class="panel-title">
<a id="compound-chebi-identifier-link" data-toggle="collapse"
data-parent="#compound-external-identifier"
href="#compound-chebi-identifier">ChEBI Identifier</a>
</h4>
</div>
<div id="compound-chebi-identifier" class="panel-collapse collapse in">
{% for eid in compound.get_chebi_identifiers %}
<a class="list-group-item"
href="{{ eid.external_url }}">CHEBI:{{ eid.identifier_value }}</a>
{% endfor %}
</div>
{% endif %}
</div>
</div>
{% endif %}
{% block action_modals %}
{% include "modals/objects/edit_compound_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/add_structure_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_set_external_reference_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="compound-detail">
<div class="panel panel-default">
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ compound.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/compound.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
<p>
The structures stored in this compound can be found at
<a target="_blank" href="{{ compound.url }}/structure" role="button"
>Compound structures &gt;&gt;</a
>
</p>
</div>
{% if compound.aliases %}
<!-- Aliases -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-aliases-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-aliases"
>Aliases</a
>
</h4>
</div>
<div id="compound-aliases" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for alias in compound.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Description -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-desc-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-desc"
>Description</a
>
</h4>
</div>
<div id="compound-desc" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ compound.description|safe }}
</div>
</div>
<!-- Image -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-image-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-image"
>Image Representation</a
>
</h4>
</div>
<div id="compound-image" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ compound.default_structure.as_svg|safe }}
</div>
</div>
</div>
<!-- SMILES -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-smiles-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-smiles"
>SMILES Representation</a
>
</h4>
</div>
<div id="compound-smiles" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ compound.default_structure.smiles }}
</div>
</div>
<!-- Canonical SMILES -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-canonical-smiles-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-canonical-smiles"
>Canonical SMILES Representation</a
>
</h4>
</div>
<div id="compound-canonical-smiles" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ compound.default_structure.canonical_smiles }}
</div>
</div>
<!-- InChiKey -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-inchi-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-inchi"
>InChIKey</a
>
</h4>
</div>
<div id="compound-inchi" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ compound.default_structure.inchikey }}
</div>
</div>
<!-- Reactions -->
{% if compound.related_reactions %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-reaction-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-reaction"
>Reactions</a
>
</h4>
</div>
<div id="compound-reaction" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for r in compound.related_reactions %}
<a class="list-group-item" href="{{ r.url }}"
>{{ r.name|safe }} <i>({{ r.package.name|safe }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Pathways -->
{% if compound.related_pathways %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-pathway-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-pathway"
>Pathways</a
>
</h4>
</div>
<div id="compound-pathway" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for r in compound.related_pathways %}
<a class="list-group-item" href="{{ r.url }}"
>{{ r.name|safe }} <i>({{ r.package.name|safe }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Scenarios -->
{% if compound.scenarios.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-scenario-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-scenario"
>Scenarios</a
>
</h4>
</div>
<div id="compound-scenario" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for s in compound.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}"
>{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
<!-- External Identifiers -->
{% if compound.get_external_identifiers %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-external-identifier-link"
data-toggle="collapse"
data-parent="#compound-detail"
href="#compound-external-identifier"
>External Identifier</a
>
</h4>
</div>
<div
id="compound-external-identifier"
class="panel-collapse in collapse"
>
<div class="panel-body list-group-item">
{% if compound.get_pubchem_compound_identifiers %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-pubchem-identifier-link"
data-toggle="collapse"
data-parent="#compound-external-identifier"
href="#compound-pubchem-identifier"
>PubChem Compound Identifier</a
>
</h4>
</div>
<div
id="compound-pubchem-identifier"
class="panel-collapse in collapse"
>
{% for eid in compound.get_pubchem_compound_identifiers %}
<a class="list-group-item" href="{{ eid.external_url }}"
>CID{{ eid.identifier_value }}</a
>
{% endfor %}
</div>
{% endif %}
{% if compound.get_pubchem_substance_identifiers %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-pubchem-identifier-link"
data-toggle="collapse"
data-parent="#compound-external-identifier"
href="#compound-pubchem-identifier"
>PubChem Substance Identifier</a
>
</h4>
</div>
<div
id="compound-pubchem-identifier"
class="panel-collapse in collapse"
>
{% for eid in compound.get_pubchem_substance_identifiers %}
<a class="list-group-item" href="{{ eid.external_url }}"
>SID{{ eid.identifier_value }}</a
>
{% endfor %}
</div>
{% endif %}
{% if compound.get_chebi_identifiers %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-chebi-identifier-link"
data-toggle="collapse"
data-parent="#compound-external-identifier"
href="#compound-chebi-identifier"
>ChEBI Identifier</a
>
</h4>
</div>
<div
id="compound-chebi-identifier"
class="panel-collapse in collapse"
>
{% for eid in compound.get_chebi_identifiers %}
<a class="list-group-item" href="{{ eid.external_url }}"
>CHEBI:{{ eid.identifier_value }}</a
>
{% endfor %}
</div>
{% endif %}
</div>
</div>
{% endif %}
</div>
</div>
{% endblock content %}

218
templates/objects/compound_structure.html
View File

@ -2,101 +2,149 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/edit_compound_structure_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_set_external_reference_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
{% block action_modals %}
{% include "modals/objects/edit_compound_structure_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_set_external_reference_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="compound-structure-detail">
<div class="panel-group" id="compound-structure-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ compound_structure.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/compound_structure.html" %}
{% endblock %}
</ul>
</div>
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ compound_structure.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/compound_structure.html" %}
{% endblock %}
</ul>
</div>
<div class="panel-body">
<p> {{ compound_structure.description|safe }} </p>
</div>
<div class="panel-body">
<p>{{ compound_structure.description|safe }}</p>
</div>
<!-- Image -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-structure-image-link"
data-toggle="collapse"
data-parent="#compound-structure-detail"
href="#compound-structure-image"
>Image Representation</a
>
</h4>
</div>
<div id="compound-structure-image" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ compound_structure.as_svg|safe }}
</div>
</div>
</div>
<!-- Image -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-structure-image-link" data-toggle="collapse" data-parent="#compound-structure-detail"
href="#compound-structure-image">Image Representation</a>
</h4>
<!-- SMILES -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-structure-smiles-link"
data-toggle="collapse"
data-parent="#compound-structure-detail"
href="#compound-structure-smiles"
>SMILES Representation</a
>
</h4>
</div>
<div id="compound-structure-smiles" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ compound_structure.smiles }}
</div>
<div id="compound-structure-image" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ compound_structure.as_svg|safe }}
</div>
</div>
</div>
{% if compound_structure.aliases %}
<!-- Aliases -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-structure-aliases-link"
data-toggle="collapse"
data-parent="#compound-structure-detail"
href="#compound-structure-aliases"
>Aliases</a
>
</h4>
</div>
<!-- SMILES -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-structure-smiles-link" data-toggle="collapse" data-parent="#compound-structure-detail"
href="#compound-structure-smiles">SMILES Representation</a>
</h4>
<div id="compound-structure-aliases" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for alias in compound_structure.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
<div id="compound-structure-smiles" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ compound_structure.smiles }}
</div>
{% endif %}
{% if compound_structure.scenarios.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="compound-structure-scenario-link"
data-toggle="collapse"
data-parent="#compound-structure-detail"
href="#compound-structure-scenario"
>Scenarios</a
>
</h4>
</div>
<div
id="compound-structure-scenario"
class="panel-collapse in collapse"
>
<div class="panel-body list-group-item">
{% for s in compound_structure.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}"
>{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if compound_structure.aliases %}
<!-- Aliases -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-structure-aliases-link" data-toggle="collapse" data-parent="#compound-structure-detail"
href="#compound-structure-aliases">Aliases</a>
</h4>
</div>
<div id="compound-structure-aliases" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for alias in compound_structure.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if compound_structure.scenarios.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="compound-structure-scenario-link" data-toggle="collapse" data-parent="#compound-structure-detail"
href="#compound-structure-scenario">Scenarios</a>
</h4>
</div>
<div id="compound-structure-scenario" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for s in compound_structure.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Reactions -->
<!-- Pathways -->
<!-- Reactions -->
<!-- Pathways -->
</div>
</div>
</div>
{% endblock content %}

336
templates/objects/edge.html
View File

@ -2,141 +2,221 @@
{% block content %}
{% block action_modals %}
{# {% include "modals/objects/edit_edge_modal.html" %}#}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
{% block action_modals %}
{# {% include "modals/objects/edit_edge_modal.html" %}#}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="edge-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ edge.edge_label.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/edge.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-group" id="edge-detail">
<div class="panel panel-default">
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ edge.edge_label.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/edge.html" %}
{% endblock %}
</ul>
</div>
</div>
<!-- Description -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="edge-desc-link" data-toggle="collapse" data-parent="#edge-detail"
href="#edge-desc">Description</a>
</h4>
</div>
<div id="edge-desc" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ edge.description|safe }}
</div>
</div>
<!-- Description -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="edge-desc-link"
data-toggle="collapse"
data-parent="#edge-detail"
href="#edge-desc"
>Description</a
>
</h4>
</div>
<div id="edge-desc" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ edge.description|safe }}
</div>
</div>
{% if edge.aliases %}
<!-- Aliases -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="edge-aliases-link" data-toggle="collapse" data-parent="#edge-detail"
href="#edge-aliases">Aliases</a>
</h4>
</div>
<div id="edge-aliases" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for alias in edge.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if edge.aliases %}
<!-- Aliases -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="edge-aliases-link"
data-toggle="collapse"
data-parent="#edge-detail"
href="#edge-aliases"
>Aliases</a
>
</h4>
</div>
<div id="edge-aliases" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for alias in edge.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Image -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="edge-image-link" data-toggle="collapse" data-parent="#edge-detail"
href="#edge-image">Image Representation</a>
</h4>
</div>
<div id="edge-image" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ edge.edge_label.as_svg|safe }}
</div>
</div>
</div>
<!-- Image -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="edge-image-link"
data-toggle="collapse"
data-parent="#edge-detail"
href="#edge-image"
>Image Representation</a
>
</h4>
</div>
<div id="edge-image" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ edge.edge_label.as_svg|safe }}
</div>
</div>
</div>
<!-- Reaction Description -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="edge-description-link" data-toggle="collapse" data-parent="#edge-description-detail"
href="#edge-description-smiles">Reaction Description</a>
</h4>
</div>
<div id="edge-description-smiles" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for educt in edge.start_nodes.all %}
<a class="btn btn-default" href="{{ educt.url }}">{{ educt.name|safe }}</a>
{% endfor %}
<span class="glyphicon glyphicon-arrow-right" style="margin-left:5em;margin-right:5em;"
aria-hidden="true"></span>
{% for product in edge.end_nodes.all %}
<a class="btn btn-default" href="{{ product.url }}">{{ product.name|safe }}</a>
{% endfor %}
</div>
</div>
<!-- Reaction Description -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="edge-description-link"
data-toggle="collapse"
data-parent="#edge-description-detail"
href="#edge-description-smiles"
>Reaction Description</a
>
</h4>
</div>
<div id="edge-description-smiles" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for educt in edge.start_nodes.all %}
<a class="btn btn-default" href="{{ educt.url }}"
>{{ educt.name|safe }}</a
>
{% endfor %}
<span
class="glyphicon glyphicon-arrow-right"
style="margin-left:5em;margin-right:5em;"
aria-hidden="true"
></span>
{% for product in edge.end_nodes.all %}
<a class="btn btn-default" href="{{ product.url }}"
>{{ product.name|safe }}</a
>
{% endfor %}
</div>
</div>
<!-- SMIRKS -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="edge-smirks-link" data-toggle="collapse" data-parent="#edge-detail"
href="#edge-smirks">SMIRKS Representation</a>
</h4>
</div>
<div id="edge-smirks" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ edge.edge_label.smirks }}
</div>
</div>
<!-- SMIRKS -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="edge-smirks-link"
data-toggle="collapse"
data-parent="#edge-detail"
href="#edge-smirks"
>SMIRKS Representation</a
>
</h4>
</div>
<div id="edge-smirks" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ edge.edge_label.smirks }}
</div>
</div>
{% if edge.edge_label.rules.all %}
<!-- Rules -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="edge-rules-link" data-toggle="collapse" data-parent="#edge-detail"
href="#edge-rules">Rules</a>
</h4>
</div>
<div id="edge-rules" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for r in edge.edge_label.rules.all %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if edge.scenarios.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="edge-scenario-link" data-toggle="collapse" data-parent="#edge-detail"
href="#edge-scenario">Scenarios</a>
</h4>
</div>
<div id="edge-scenario" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for s in edge.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
{% if edge.edge_label.rules.all %}
<!-- Rules -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="edge-rules-link"
data-toggle="collapse"
data-parent="#edge-detail"
href="#edge-rules"
>Rules</a
>
</h4>
</div>
<div id="edge-rules" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for r in edge.edge_label.rules.all %}
<a class="list-group-item" href="{{ r.url }}"
>{{ r.name|safe }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if edge.scenarios.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="edge-scenario-link"
data-toggle="collapse"
data-parent="#edge-detail"
href="#edge-scenario"
>Scenarios</a
>
</h4>
</div>
<div id="edge-scenario" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for s in edge.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}"
>{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
</div>
</div>
{% endblock content %}

253
templates/objects/enzymelink.html
View File

@ -1,105 +1,164 @@
{% extends "framework.html" %}
{% block content %}
<div class="panel-group" id="enzyme-detail">
<div class="panel panel-default">
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ enzymelink.ec_number }}
</div>
<div class="panel-group" id="enzyme-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ enzymelink.ec_number }}
</div>
<!-- Name -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="enzyme-name-link" data-toggle="collapse" data-parent="#enzyme-detail"
href="#enzyme-name">Enzyme Name</a>
</h4>
</div>
<div id="enzyme-name" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ enzymelink.name }}
</div>
</div>
<!-- Linking Method -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="enzyme-linking-link" data-toggle="collapse" data-parent="#enzyme-detail"
href="#enzyme-linking">Linking Method</a>
</h4>
</div>
<div id="enzyme-linking" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ enzymelink.linking_method }}. &nbsp;<a
href="https://wiki.envipath.org/index.php/Rules#EnzymeLinks" target="#">Learn more &gt;&gt;</a>
</div>
</div>
{% if enzymelink.kegg_reaction_links %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="enzyme-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
href="#enzyme-evidence">Linking Evidence</a>
</h4>
</div>
<div id="enzyme-evidence" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for kl in enzymelink.kegg_reaction_links %}
<a class="list-group-item"
href="{{ kl.external_url }}">{{ kl.identifier_value }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if enzymelink.reaction_evidence.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="enzyme-reaction-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
href="#enzyme-reaction-evidence">Linking Evidence - enviPath Reactions</a>
</h4>
</div>
<div id="enzyme-reaction-evidence" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for r in enzymelink.reaction_evidence.all %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
{% if enzymelink.edge_evidence.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="enzyme-edge-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
href="#enzyme-edge-evidence">Linking Evidence - enviPath Pathways</a>
</h4>
</div>
<div id="enzyme-edge-evidence" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for e in enzymelink.edge_evidence.all %}
<a class="list-group-item" href="{{ e.pathway.url }}">{{ e.pathway.name }}
<i>({{ r.package.name }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- External DB Reference -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="enzyme-external-identifier-link" data-toggle="collapse" data-parent="#enzyme-detail"
href="#enzyme-external-identifier">External DB References</a>
</h4>
</div>
<div id="enzyme-external-identifier" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<a class="list-group-item"
href="http://www.brenda-enzymes.org/enzyme.php?ecno={{ enzymelink.ec_number }}"
target="_blank"> Brenda entry for {{ enzymelink.ec_number }}</a>
</div>
</div>
<!-- Name -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="enzyme-name-link"
data-toggle="collapse"
data-parent="#enzyme-detail"
href="#enzyme-name"
>Enzyme Name</a
>
</h4>
</div>
<div id="enzyme-name" class="panel-collapse in collapse">
<div class="panel-body list-group-item">{{ enzymelink.name }}</div>
</div>
<!-- Linking Method -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="enzyme-linking-link"
data-toggle="collapse"
data-parent="#enzyme-detail"
href="#enzyme-linking"
>Linking Method</a
>
</h4>
</div>
<div id="enzyme-linking" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ enzymelink.linking_method }}. &nbsp;<a
href="https://wiki.envipath.org/index.php/Rules#EnzymeLinks"
target="#"
>Learn more &gt;&gt;</a
>
</div>
</div>
{% if enzymelink.kegg_reaction_links %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="enzyme-evidence-link"
data-toggle="collapse"
data-parent="#enzyme-detail"
href="#enzyme-evidence"
>Linking Evidence</a
>
</h4>
</div>
<div id="enzyme-evidence" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for kl in enzymelink.kegg_reaction_links %}
<a class="list-group-item" href="{{ kl.external_url }}"
>{{ kl.identifier_value }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if enzymelink.reaction_evidence.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="enzyme-reaction-evidence-link"
data-toggle="collapse"
data-parent="#enzyme-detail"
href="#enzyme-reaction-evidence"
>Linking Evidence - enviPath Reactions</a
>
</h4>
</div>
<div id="enzyme-reaction-evidence" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for r in enzymelink.reaction_evidence.all %}
<a class="list-group-item" href="{{ r.url }}"
>{{ r.name }} <i>({{ r.package.name }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if enzymelink.edge_evidence.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="enzyme-edge-evidence-link"
data-toggle="collapse"
data-parent="#enzyme-detail"
href="#enzyme-edge-evidence"
>Linking Evidence - enviPath Pathways</a
>
</h4>
</div>
<div id="enzyme-edge-evidence" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for e in enzymelink.edge_evidence.all %}
<a class="list-group-item" href="{{ e.pathway.url }}"
>{{ e.pathway.name }} <i>({{ r.package.name }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
<!-- External DB Reference -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="enzyme-external-identifier-link"
data-toggle="collapse"
data-parent="#enzyme-detail"
href="#enzyme-external-identifier"
>External DB References</a
>
</h4>
</div>
<div id="enzyme-external-identifier" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<a
class="list-group-item"
href="http://www.brenda-enzymes.org/enzyme.php?ecno={{ enzymelink.ec_number }}"
target="_blank"
>
Brenda entry for {{ enzymelink.ec_number }}</a
>
</div>
</div>
</div>
</div>
{% endblock content %}

117
templates/objects/group.html
View File

@ -2,63 +2,90 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/edit_group_modal.html" %}
{% include "modals/objects/edit_group_member_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
{% block action_modals %}
{% include "modals/objects/edit_group_modal.html" %}
{% include "modals/objects/edit_group_member_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="package-detail">
<div class="panel-group" id="package-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ group.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/group.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
<p> {{ group.description|safe }} </p>
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ group.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/group.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
<p>{{ group.description|safe }}</p>
</div>
</div>
<p></p>
<div class="panel panel-default">
<div id="member-panel" style="font-size:2rem;height: 46px" class="panel-heading">Members</div>
<div class="panel-body">
<p>List of members of this group</p>
</div>
<ul class="list-group">
{% for um in group.user_member.all %}
<a class="list-group-item" href="{{ um.url }}">{{ um.username|safe }}</a>
{% endfor %}
{% for gm in group.group_member.all %}
<a class="list-group-item" href="{{ gm.url }}">{{ gm.name|safe }}</a>
{% endfor %}
</ul>
<div
id="member-panel"
style="font-size:2rem;height: 46px"
class="panel-heading"
>
Members
</div>
<div class="panel-body">
<p>List of members of this group</p>
</div>
<ul class="list-group">
{% for um in group.user_member.all %}
<a class="list-group-item" href="{{ um.url }}"
>{{ um.username|safe }}</a
>
{% endfor %}
{% for gm in group.group_member.all %}
<a class="list-group-item" href="{{ gm.url }}">{{ gm.name|safe }}</a>
{% endfor %}
</ul>
</div>
<p></p>
<div class="panel panel-default">
<div id="package-panel" style="font-size:2rem;height: 46px" class="panel-heading">Packages</div>
<div class="panel-body">
<p>Packages where this group has access to</p>
</div>
<ul class="list-group">
{% for p in packages %}
<a class="list-group-item" href="{{ p.url }}">{{ p.name|safe }}</a>
{% endfor %}
</ul>
<div
id="package-panel"
style="font-size:2rem;height: 46px"
class="panel-heading"
>
Packages
</div>
<div class="panel-body">
<p>Packages where this group has access to</p>
</div>
<ul class="list-group">
{% for p in packages %}
<a class="list-group-item" href="{{ p.url }}">{{ p.name|safe }}</a>
{% endfor %}
</ul>
</div>
</div>
</div>
{% endblock content %}

14
templates/objects/model.html
View File

@ -67,7 +67,7 @@
>
</h4>
</div>
<div id="rule-package" class="panel-collapse collapse in">
<div id="rule-package" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for p in model.rule_packages.all %}
<a class="list-group-item" href="{{ p.url }}"
@ -91,7 +91,7 @@
>
</h4>
</div>
<div id="reaction-package" class="panel-collapse collapse in">
<div id="reaction-package" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for p in model.data_packages.all %}
<a class="list-group-item" href="{{ p.url }}"
@ -116,7 +116,7 @@
>
</h4>
</div>
<div id="eval-package" class="panel-collapse collapse in">
<div id="eval-package" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for p in model.eval_packages.all %}
<a class="list-group-item" href="{{ p.url }}"
@ -141,7 +141,7 @@
>
</h4>
</div>
<div id="model-status" class="panel-collapse collapse in">
<div id="model-status" class="panel-collapse in collapse">
<div class="panel-body list-group-item">{{ model.status }}</div>
</div>
{% endif %}
@ -161,7 +161,7 @@
>
</h4>
</div>
<div id="predict-smiles" class="panel-collapse collapse in">
<div id="predict-smiles" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<div class="input-group">
<input
@ -203,7 +203,7 @@
>
</h4>
</div>
<div id="app-domain-assessment" class="panel-collapse collapse in">
<div id="app-domain-assessment" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<div class="input-group">
<input
@ -245,7 +245,7 @@
>
</h4>
</div>
<div id="sg-curve" class="panel-collapse collapse in">
<div id="sg-curve" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<!-- Center container contents -->
<div

260
templates/objects/node.html
View File

@ -2,120 +2,174 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/edit_node_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
{% block action_modals %}
{% include "modals/objects/edit_node_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="node-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ node.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/node.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
The underlying structure can be found <a href="{{ node.default_node_label.url }}">here</a>.
</div>
<div class="panel-group" id="node-detail">
<div class="panel panel-default">
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ node.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/node.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
The underlying structure can be found
<a href="{{ node.default_node_label.url }}">here</a>.
</div>
<!-- Description -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="node-desc-link" data-toggle="collapse" data-parent="#node-detail"
href="#node-desc">Description</a>
</h4>
</div>
<div id="node-desc" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ node.description|safe }}
</div>
</div>
<!-- Description -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="node-desc-link"
data-toggle="collapse"
data-parent="#node-detail"
href="#node-desc"
>Description</a
>
</h4>
</div>
<div id="node-desc" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ node.description|safe }}
</div>
</div>
{% if node.aliases %}
<!-- Aliases -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="node-aliases-link" data-toggle="collapse" data-parent="#node-detail"
href="#node-aliases">Aliases</a>
</h4>
</div>
<div id="node-aliases" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for alias in node.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if node.aliases %}
<!-- Aliases -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="node-aliases-link"
data-toggle="collapse"
data-parent="#node-detail"
href="#node-aliases"
>Aliases</a
>
</h4>
</div>
<div id="node-aliases" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for alias in node.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Image -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="node-image-link" data-toggle="collapse" data-parent="#node-detail"
href="#node-image">Image Representation</a>
</h4>
</div>
<div id="node-image" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ node.default_node_label.as_svg|safe }}
</div>
</div>
</div>
<!-- Image -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="node-image-link"
data-toggle="collapse"
data-parent="#node-detail"
href="#node-image"
>Image Representation</a
>
</h4>
</div>
<div id="node-image" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ node.default_node_label.as_svg|safe }}
</div>
</div>
</div>
<!-- SMILES -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="node-smiles-link" data-toggle="collapse" data-parent="#node-detail"
href="#node-smiles">SMILES Representation</a>
</h4>
</div>
<div id="node-smiles" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ node.default_node_label.smiles }}
</div>
</div>
<!-- SMILES -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="node-smiles-link"
data-toggle="collapse"
data-parent="#node-detail"
href="#node-smiles"
>SMILES Representation</a
>
</h4>
</div>
<div id="node-smiles" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ node.default_node_label.smiles }}
</div>
</div>
{% if node.scenarios.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="node-scenario-link" data-toggle="collapse" data-parent="#node-detail"
href="#node-scenario">Scenarios</a>
</h4>
</div>
<div id="node-scenario" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for s in node.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
{% if node.scenarios.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="node-scenario-link"
data-toggle="collapse"
data-parent="#node-detail"
href="#node-scenario"
>Scenarios</a
>
</h4>
</div>
<div id="node-scenario" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for s in node.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}"
>{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if app_domain_assessment_data %}
<div id="appDomainAssessmentResultTable"></div>
{% if app_domain_assessment_data %}
<div id="appDomainAssessmentResultTable"></div>
{# prettier-ignore-start #}
<script>
$(document).ready(function () {
handleAssessmentResponse("{% url 'depict' %}", {{ app_domain_assessment_data|safe }})
})
</script>
{% endif %}
</div>
{# prettier-ignore-end #}
{% endif %}
</div>
</div>
{% endblock content %}

107
templates/objects/package.html
View File

@ -2,57 +2,78 @@
{% block content %}
{% block action_modals %}
{% block action_modals %}
{% include "modals/objects/edit_package_modal.html" %}
{% include "modals/objects/edit_package_permissions_modal.html" %}
{% include "modals/objects/publish_package_modal.html" %}
{% include "modals/objects/set_license_modal.html" %}
{% include "modals/objects/export_package_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
{% endblock action_modals %}
<div class="panel-group" id="package-detail">
<div class="panel-group" id="package-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ package.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/package.html" %}
{% endblock %}
</ul>
</div>
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ package.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/package.html" %}
{% endblock %}
</ul>
</div>
<div class="panel-body">
<p> {{ package.description|safe }} </p>
</div>
<ul class="list-group">
<li class="list-group-item">
<a href="{{ package.url }}/pathway">Pathways ({{ package.pathways.count }})</a>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/rule">Rules ({{ package.rules.count }})</a>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/compound">Compounds ({{ package.compounds.count }})</a>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/reaction">Reactions ({{ package.reactions.count }})</a>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/model">Models ({{ package.models.count }})</a>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/scenario">Scenarios ({{ package.scenarios.count }})</a>
</li>
</ul>
</div>
<div class="panel-body">
<p>{{ package.description|safe }}</p>
</div>
<ul class="list-group">
<li class="list-group-item">
<a href="{{ package.url }}/pathway"
>Pathways ({{ package.pathways.count }})</a
>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/rule">Rules ({{ package.rules.count }})</a>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/compound"
>Compounds ({{ package.compounds.count }})</a
>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/reaction"
>Reactions ({{ package.reactions.count }})</a
>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/model"
>Models ({{ package.models.count }})</a
>
</li>
<li class="list-group-item">
<a href="{{ package.url }}/scenario"
>Scenarios ({{ package.scenarios.count }})</a
>
</li>
</ul>
</div>
</div>
</div>
{% endblock content %}

746
templates/objects/pathway.html
View File

@ -1,338 +1,449 @@
{% extends "framework.html" %}
{% load static %}
{% block content %}
<script src="https://d3js.org/d3.v7.min.js"></script>
<style>
#vizdiv {
width: 100%;
height: 600px;
background: white;
}
<script src="https://d3js.org/d3.v7.min.js"></script>
<style>
#vizdiv {
width: 100%;
height: 600px;
background: white;
}
#pwsvg {
width: 100%;
height: 100%;
color: red;
}
#pwsvg {
width: 100%;
height: 100%;
color: red;
}
.link {
stroke: #999;
stroke-opacity: 0.6;
}
.link {
stroke: #999;
stroke-opacity: 0.6;
//marker-end: url(#arrow);
}
.link_no_arrow {
stroke: #999;
stroke-opacity: 0.6;
}
.link_no_arrow {
stroke: #999;
stroke-opacity: 0.6;
}
.node image {
cursor: pointer;
}
.node image {
cursor: pointer;
}
.node circle {
fill: lightblue;
stroke: steelblue;
stroke-width: 1.5px;
}
.node circle {
fill: lightblue;
stroke: steelblue;
stroke-width: 1.5px;
}
.inside_app_domain {
fill: green;
stroke: green;
stroke-width: 1.5px;
}
.inside_app_domain {
fill: green;
stroke: green;
stroke-width: 1.5px;
}
.outside_app_domain {
fill: red;
stroke: red;
stroke-width: 1.5px;
}
.outside_app_domain {
fill: red;
stroke: red;
stroke-width: 1.5px;
}
.passes_app_domain {
stroke: green;
stroke-width: 1.5px;
stroke-opacity: 0.6;
}
.passes_app_domain {
stroke: green;
stroke-width: 1.5px;
stroke-opacity: 0.6;
}
.fails_app_domain {
stroke: red;
stroke-width: 1.5px;
stroke-opacity: 0.6;
}
.fails_app_domain {
stroke: red;
stroke-width: 1.5px;
stroke-opacity: 0.6;
}
.highlighted {
stroke: red;
stroke-width: 3px;
}
.tooltip {
position: absolute;
background: lightgrey;
padding: 5px;
border-radius: 5px;
visibility: hidden;
opacity: 1;
}
</style>
<script src="{% static 'js/pw.js' %}"></script>
.highlighted {
stroke: red;
stroke-width: 3px;
}
{% block action_modals %}
{% include "modals/objects/add_pathway_node_modal.html" %}
{% include "modals/objects/add_pathway_edge_modal.html" %}
{% include "modals/objects/download_pathway_csv_modal.html" %}
{% include "modals/objects/download_pathway_image_modal.html" %}
{% include "modals/objects/identify_missing_rules_modal.html" %}
{% include "modals/objects/generic_copy_object_modal.html" %}
{% include "modals/objects/edit_pathway_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/delete_pathway_node_modal.html" %}
{% include "modals/objects/delete_pathway_edge_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
.tooltip {
position: absolute;
background: lightgrey;
padding: 5px;
border-radius: 5px;
visibility: hidden;
opacity: 1
}
</style>
<script src="{% static 'js/pw.js' %}"></script>
{% block action_modals %}
{% include "modals/objects/add_pathway_node_modal.html" %}
{% include "modals/objects/add_pathway_edge_modal.html" %}
{% include "modals/objects/download_pathway_csv_modal.html" %}
{% include "modals/objects/download_pathway_image_modal.html" %}
{% include "modals/objects/identify_missing_rules_modal.html" %}
{% include "modals/objects/generic_copy_object_modal.html" %}
{% include "modals/objects/edit_pathway_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/delete_pathway_node_modal.html" %}
{% include "modals/objects/delete_pathway_edge_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<p></p>
<div id="pwcontent">
<div class="panel-group" id="pwAccordion">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ pathway.name|safe }}
</div>
</div>
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="vizLink" data-toggle="collapse" data-parent="#pwAccordion" href="#viz">
Graphical Representation
</a>
</h4>
</div>
<div id="viz" class="panel-collapse collapse in">
<nav role="navigation" class="navbar navbar-default" style="margin: 0;">
<div class="navbar-header">
</div>
<div id="editbarCollapse" class="collapse navbar-collapse ">
<ul class="nav navbar-nav">
<li class="dropdown requiresWritePerm">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-haspopup="true" aria-expanded="false">
<span class="glyphicon glyphicon-edit"></span>
Edit
<span class="caret"></span></a>
<ul id="editingList" class="dropdown-menu">
{% block actions %}
{% include "actions/objects/pathway.html" %}
{% endblock %}
</ul>
</li>
{% if pathway.setting.model.app_domain %}
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-haspopup="true" aria-expanded="false">
<span class="glyphicon glyphicon-eye-open"></span>
View
<span class="caret"></span></a>
<ul id="editingList" class="dropdown-menu">
<li>
<a class="button" id="app-domain-toggle-button">
<i id="app-domain-toggle-button" class="glyphicon glyphicon-eye-open"></i> App Domain View</a>
</li>
</ul>
</li>
{% endif %}
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a role="button" data-toggle="modal" onclick="goFullscreen('vizdiv')">
<span class="glyphicon glyphicon-fullscreen"></span>
Fullscreen
</a>
</li>
<li>
{% if pathway.completed %}
<button type="button" class="btn btn-default navbar-btn" data-toggle="popover"
id="status" data-original-title="" title=""
data-content="Pathway prediction complete.">
<span class="glyphicon glyphicon-ok"></span>
</button>
{% elif pathway.failed %}
<button type="button" class="btn btn-default navbar-btn" data-toggle="popover"
id="status" data-original-title="" title=""
data-content="Pathway prediction failed.">
<span class="glyphicon glyphicon-remove"></span>
</button>
{% else %}
<button type="button" class="btn btn-default navbar-btn" data-toggle="popover"
id="status" data-original-title="" title=""
data-content="Pathway prediction running.">
<img height="20" src="{% static '/images/wait.gif' %}">
</button>
{% endif %}
&nbsp;
</li>
</ul>
</div>
</nav>
<div id="vizdiv" >
<svg id="pwsvg">
<defs>
<marker id="arrow" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
orient="auto-start-reverse" markerUnits="userSpaceOnUse">
<path d="M 0 0 L 10 5 L 0 10 z" fill="#999"/>
</marker>
<marker id="arrow_passes_app_domain" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
orient="auto-start-reverse" markerUnits="userSpaceOnUse">
<path d="M 0 0 L 10 5 L 0 10 z" fill="green"/>
</marker>
<marker id="arrow_fails_app_domain" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
orient="auto-start-reverse" markerUnits="userSpaceOnUse">
<path d="M 0 0 L 10 5 L 0 10 z" fill="red"/>
</marker>
</defs>
<g id="zoomable"></g>
</svg>
<div id="tooltip" class="tooltip"></div>
</div>
</div>
<!-- Description -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="DescriptionLink" data-toggle="collapse" data-parent="#pathwayAccordion"
href="#Description">Description</a></h4>
</div>
<div id="Description" class="panel-collapse collapse in">
<div class="panel-body list-group-item" id="DescriptionContent">
{{ pathway.description | safe }}
</div>
</div>
{% if pathway.aliases %}
<!-- Aliases -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="pathway-aliases-link" data-toggle="collapse" data-parent="#pathway-detail"
href="#pathway-aliases">Aliases</a>
</h4>
</div>
<div id="pathway-aliases" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for alias in pathway.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if pathway.scenarios.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="pathway-scenario-link" data-toggle="collapse" data-parent="#pathway-detail"
href="#pathway-scenario">Scenarios</a>
</h4>
</div>
<div id="pathway-scenario" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for s in pathway.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
{% if pathway.setting %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="pathwaySettingLink" data-toggle="collapse" data-parent="#pathwayAccordion"
href="#pathwaySetting">Setting</a></h4>
</div>
<div id="pathwaySetting" class="panel-collapse collapse">
<div class="panel-body list-group-item" id="pathwaySettingContent">
<table class="table table-bordered table-hover">
<tr style="background-color: rgba(0, 0, 0, 0.08);">
<th scope="col" width="20%">Parameter</th>
<th scope="col" width="80%">Value</th>
</tr>
<tbody>
{% if pathway.setting.model %}
<tr>
<td width="20%">Model</td>
<td width="80%">
<table width="100%" class="table table-bordered table-hover">
<tbody>
<tr>
<td colspan="2">
<li class="list-group-item">
<a href="{{ pathway.setting.model.url }}">
{{ pathway.setting.model.name|safe }}
</a>
</li>
</td>
</tr>
<tr>
<th width="20%">Model Parameter</th>
<th width="80%">Parameter Value</th>
</tr>
<tr>
<td width="20%">
Threshold
</td>
<td width="80%">
{{ pathway.setting.model_threshold }}
</td>
</tr>
</tbody>
</table>
</td>
</tr>
{% endif %}
{% if pathway.setting.rule_packages.all %}
<tr>
<td width="20%">Rule Packages</td>
<td width="80%">
<table width="100%" class="table table-bordered table-hover">
<tbody>
<tr>
<td colspan="2">
{% for p in pathway.setting.rule_packages.all %}
<li class="list-group-item">
<a href="{{ p.url }}">
{{ p.name|safe }}
</a>
</li>
{% endfor %}
</td>
</tr>
</tbody>
</table>
</td>
</tr>
{% endif %}
<tr>
<td>
<p>Max Nodes</p>
</td>
<td>
<p>{{ pathway.setting.max_nodes }}</p>
</td>
</tr>
<tr>
<td>
<p>Max Depth</p>
</td>
<td>
<p>{{ pathway.setting.max_depth }}</p>
</td>
</tr>
</tbody>
</table>
</div>
</div>
{% endif %}
<p></p>
<div id="pwcontent">
<div class="panel-group" id="pwAccordion">
<div class="panel panel-default">
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ pathway.name|safe }}
</div>
</div>
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="vizLink"
data-toggle="collapse"
data-parent="#pwAccordion"
href="#viz"
>
Graphical Representation
</a>
</h4>
</div>
<div id="viz" class="panel-collapse in collapse">
<nav role="navigation" class="navbar navbar-default" style="margin: 0;">
<div class="navbar-header"></div>
<div id="editbarCollapse" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li class="dropdown requiresWritePerm">
<a
href="#"
class="dropdown-toggle"
data-toggle="dropdown"
role="button"
aria-haspopup="true"
aria-expanded="false"
>
<span class="glyphicon glyphicon-edit"></span>
Edit
<span class="caret"></span
></a>
<ul id="editingList" class="dropdown-menu">
{% block actions %}
{% include "actions/objects/pathway.html" %}
{% endblock %}
</ul>
</li>
{% if pathway.setting.model.app_domain %}
<li class="dropdown">
<a
href="#"
class="dropdown-toggle"
data-toggle="dropdown"
role="button"
aria-haspopup="true"
aria-expanded="false"
>
<span class="glyphicon glyphicon-eye-open"></span>
View
<span class="caret"></span
></a>
<ul id="editingList" class="dropdown-menu">
<li>
<a class="button" id="app-domain-toggle-button">
<i
id="app-domain-toggle-button"
class="glyphicon glyphicon-eye-open"
></i>
App Domain View</a
>
</li>
</ul>
</li>
{% endif %}
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a
role="button"
data-toggle="modal"
onclick="goFullscreen('vizdiv')"
>
<span class="glyphicon glyphicon-fullscreen"></span>
Fullscreen
</a>
</li>
<li>
{% if pathway.completed %}
<button
type="button"
class="btn btn-default navbar-btn"
data-toggle="popover"
id="status"
data-original-title=""
title=""
data-content="Pathway prediction complete."
>
<span class="glyphicon glyphicon-ok"></span>
</button>
{% elif pathway.failed %}
<button
type="button"
class="btn btn-default navbar-btn"
data-toggle="popover"
id="status"
data-original-title=""
title=""
data-content="Pathway prediction failed."
>
<span class="glyphicon glyphicon-remove"></span>
</button>
{% else %}
<button
type="button"
class="btn btn-default navbar-btn"
data-toggle="popover"
id="status"
data-original-title=""
title=""
data-content="Pathway prediction running."
>
<img height="20" src="{% static '/images/wait.gif' %}" />
</button>
{% endif %}
&nbsp;
</li>
</ul>
</div>
</nav>
<div id="vizdiv">
<svg id="pwsvg">
<defs>
<marker
id="arrow"
viewBox="0 0 10 10"
refX="43"
refY="5"
markerWidth="6"
markerHeight="6"
orient="auto-start-reverse"
markerUnits="userSpaceOnUse"
>
<path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
</marker>
<marker
id="arrow_passes_app_domain"
viewBox="0 0 10 10"
refX="43"
refY="5"
markerWidth="6"
markerHeight="6"
orient="auto-start-reverse"
markerUnits="userSpaceOnUse"
>
<path d="M 0 0 L 10 5 L 0 10 z" fill="green" />
</marker>
<marker
id="arrow_fails_app_domain"
viewBox="0 0 10 10"
refX="43"
refY="5"
markerWidth="6"
markerHeight="6"
orient="auto-start-reverse"
markerUnits="userSpaceOnUse"
>
<path d="M 0 0 L 10 5 L 0 10 z" fill="red" />
</marker>
</defs>
<g id="zoomable"></g>
</svg>
<div id="tooltip" class="tooltip"></div>
</div>
</div>
<!-- Description -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="DescriptionLink"
data-toggle="collapse"
data-parent="#pathwayAccordion"
href="#Description"
>Description</a
>
</h4>
</div>
<div id="Description" class="panel-collapse in collapse">
<div class="panel-body list-group-item" id="DescriptionContent">
{{ pathway.description | safe }}
</div>
</div>
{% if pathway.aliases %}
<!-- Aliases -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="pathway-aliases-link"
data-toggle="collapse"
data-parent="#pathway-detail"
href="#pathway-aliases"
>Aliases</a
>
</h4>
</div>
<div id="pathway-aliases" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for alias in pathway.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if pathway.scenarios.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="pathway-scenario-link"
data-toggle="collapse"
data-parent="#pathway-detail"
href="#pathway-scenario"
>Scenarios</a
>
</h4>
</div>
<div id="pathway-scenario" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for s in pathway.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}"
>{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if pathway.setting %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="pathwaySettingLink"
data-toggle="collapse"
data-parent="#pathwayAccordion"
href="#pathwaySetting"
>Setting</a
>
</h4>
</div>
<div id="pathwaySetting" class="panel-collapse collapse">
<div class="panel-body list-group-item" id="pathwaySettingContent">
<table class="table-bordered table-hover table">
<tr style="background-color: rgba(0, 0, 0, 0.08);">
<th scope="col" width="20%">Parameter</th>
<th scope="col" width="80%">Value</th>
</tr>
<tbody>
{% if pathway.setting.model %}
<tr>
<td width="20%">Model</td>
<td width="80%">
<table
width="100%"
class="table-bordered table-hover table"
>
<tbody>
<tr>
<td colspan="2">
<li class="list-group-item">
<a href="{{ pathway.setting.model.url }}">
{{ pathway.setting.model.name|safe }}
</a>
</li>
</td>
</tr>
<tr>
<th width="20%">Model Parameter</th>
<th width="80%">Parameter Value</th>
</tr>
<tr>
<td width="20%">Threshold</td>
<td width="80%">
{{ pathway.setting.model_threshold }}
</td>
</tr>
</tbody>
</table>
</td>
</tr>
{% endif %}
{% if pathway.setting.rule_packages.all %}
<tr>
<td width="20%">Rule Packages</td>
<td width="80%">
<table
width="100%"
class="table-bordered table-hover table"
>
<tbody>
<tr>
<td colspan="2">
{% for p in pathway.setting.rule_packages.all %}
<li class="list-group-item">
<a href="{{ p.url }}"> {{ p.name|safe }} </a>
</li>
{% endfor %}
</td>
</tr>
</tbody>
</table>
</td>
</tr>
{% endif %}
<tr>
<td>
<p>Max Nodes</p>
</td>
<td>
<p>{{ pathway.setting.max_nodes }}</p>
</td>
</tr>
<tr>
<td>
<p>Max Depth</p>
</td>
<td>
<p>{{ pathway.setting.max_depth }}</p>
</td>
</tr>
</tbody>
</table>
</div>
</div>
{% endif %}
</div>
</div>
{# prettier-ignore-start #}
<script>
// Global switch for app domain view
var appDomainViewEnabled = false;
@ -455,4 +566,5 @@
});
</script>
{# prettier-ignore-end #}
{% endblock content %}

562
templates/objects/reaction.html
View File

@ -2,224 +2,352 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/edit_reaction_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_set_external_reference_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="reaction-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ reaction.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/reaction.html" %}
{% endblock %}
</ul>
</div>
</div>
<!-- Description -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-desc-link" data-toggle="collapse" data-parent="#reaction-detail"
href="#reaction-desc">Description</a>
</h4>
</div>
<div id="reaction-desc" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ reaction.description|safe }}
</div>
</div>
{% if reaction.aliases %}
<!-- Aliases -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-aliases-link" data-toggle="collapse" data-parent="#reaction-detail"
href="#reaction-aliases">Aliases</a>
</h4>
</div>
<div id="reaction-aliases" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for alias in reaction.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Image -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-image-link" data-toggle="collapse" data-parent="#reaction-detail"
href="#reaction-image">Image Representation</a>
</h4>
</div>
<div id="reaction-image" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ reaction.as_svg|safe }}
</div>
</div>
</div>
<!-- Reaction Description -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-description-link" data-toggle="collapse" data-parent="#reaction-description-detail"
href="#reaction-description-smiles">Reaction Description</a>
</h4>
</div>
<div id="reaction-description-smiles" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for educt in reaction.educts.all %}
<a class="btn btn-default" href="{{ educt.url }}">{{ educt.name|safe }}</a>
{% endfor %}
<span class="glyphicon glyphicon-arrow-right" style="margin-left:5em;margin-right:5em;"
aria-hidden="true"></span>
{% for product in reaction.products.all %}
<a class="btn btn-default" href="{{ product.url }}">{{ product.name|safe }}</a>
{% endfor %}
</div>
</div>
<!-- SMIRKS -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-smirks-link" data-toggle="collapse" data-parent="#reaction-detail"
href="#reaction-smirks">SMIRKS Representation</a>
</h4>
</div>
<div id="reaction-smirks" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{{ reaction.smirks }}
</div>
</div>
{% if reaction.rules.all %}
<!-- Rules -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-rules-link" data-toggle="collapse" data-parent="#reaction-detail"
href="#reaction-rules">Rules</a>
</h4>
</div>
<div id="reaction-rules" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for r in reaction.rules.all %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if reaction.get_related_enzymes %}
<!-- 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 e in reaction.get_related_enzymes %}
<a class="list-group-item" href="http://www.brenda-enzymes.org/enzyme.php?ecno={{ e.ec_number }}">{{ e.name }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if reaction.related_pathways %}
<!-- Pathways -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-pathway-link" data-toggle="collapse" data-parent="#reaction-detail"
href="#reaction-pathway">Pathways</a>
</h4>
</div>
<div id="reaction-pathway" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for r in reaction.related_pathways %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if reaction.scenarios.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-scenario-link" data-toggle="collapse" data-parent="#reaction-detail"
href="#reaction-scenario">Scenarios</a>
</h4>
</div>
<div id="reaction-scenario" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for s in reaction.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- External Identifiers -->
{% if reaction.get_external_identifiers %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-external-identifier-link" data-toggle="collapse" data-parent="#reaction-detail"
href="#reaction-external-identifier">External Identifier</a>
</h4>
</div>
<div id="reaction-external-identifier" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% if reaction.get_rhea_identifiers %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-rhea-identifier-link" data-toggle="collapse"
data-parent="#reaction-external-identifier"
href="#reaction-rhea-identifier">Rhea</a>
</h4>
</div>
<div id="reaction-rhea-identifier" class="panel-collapse collapse in">
{% for eid in reaction.get_rhea_identifiers %}
<a class="list-group-item"
href="{{ eid.external_url }}">{{ eid.identifier_value }}</a>
{% endfor %}
</div>
{% endif %}
{% if reaction.get_uniprot_identifiers %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">
<h4 class="panel-title">
<a id="reaction-uniprot-identifier-link" data-toggle="collapse"
data-parent="#reaction-external-identifier"
href="#reaction-uniprot-identifier">UniProt</a>
</h4>
</div>
<div id="reaction-uniprot-identifier" class="panel-collapse collapse in">
{% for eid in reaction.get_uniprot_identifiers %}
<a class="list-group-item"
href="{{ eid.external_url }}">10 SwissProt entries ({{ eid.identifier_value }})</a>
{% endfor %}
</div>
{% endif %}
</div>
</div>
{% endif %}
{% block action_modals %}
{% include "modals/objects/edit_reaction_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_set_external_reference_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="reaction-detail">
<div class="panel panel-default">
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ reaction.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/reaction.html" %}
{% endblock %}
</ul>
</div>
</div>
<!-- Description -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-desc-link"
data-toggle="collapse"
data-parent="#reaction-detail"
href="#reaction-desc"
>Description</a
>
</h4>
</div>
<div id="reaction-desc" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{{ reaction.description|safe }}
</div>
</div>
{% if reaction.aliases %}
<!-- Aliases -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-aliases-link"
data-toggle="collapse"
data-parent="#reaction-detail"
href="#reaction-aliases"
>Aliases</a
>
</h4>
</div>
<div id="reaction-aliases" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for alias in reaction.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Image -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-image-link"
data-toggle="collapse"
data-parent="#reaction-detail"
href="#reaction-image"
>Image Representation</a
>
</h4>
</div>
<div id="reaction-image" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<div id="image-div" align="center">{{ reaction.as_svg|safe }}</div>
</div>
</div>
<!-- Reaction Description -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-description-link"
data-toggle="collapse"
data-parent="#reaction-description-detail"
href="#reaction-description-smiles"
>Reaction Description</a
>
</h4>
</div>
<div id="reaction-description-smiles" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for educt in reaction.educts.all %}
<a class="btn btn-default" href="{{ educt.url }}"
>{{ educt.name|safe }}</a
>
{% endfor %}
<span
class="glyphicon glyphicon-arrow-right"
style="margin-left:5em;margin-right:5em;"
aria-hidden="true"
></span>
{% for product in reaction.products.all %}
<a class="btn btn-default" href="{{ product.url }}"
>{{ product.name|safe }}</a
>
{% endfor %}
</div>
</div>
<!-- SMIRKS -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-smirks-link"
data-toggle="collapse"
data-parent="#reaction-detail"
href="#reaction-smirks"
>SMIRKS Representation</a
>
</h4>
</div>
<div id="reaction-smirks" class="panel-collapse in collapse">
<div class="panel-body list-group-item">{{ reaction.smirks }}</div>
</div>
{% if reaction.rules.all %}
<!-- Rules -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-rules-link"
data-toggle="collapse"
data-parent="#reaction-detail"
href="#reaction-rules"
>Rules</a
>
</h4>
</div>
<div id="reaction-rules" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for r in reaction.rules.all %}
<a class="list-group-item" href="{{ r.url }}"
>{{ r.name|safe }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if reaction.get_related_enzymes %}
<!-- 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 e in reaction.get_related_enzymes %}
<a
class="list-group-item"
href="http://www.brenda-enzymes.org/enzyme.php?ecno={{ e.ec_number }}"
>{{ e.name }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if reaction.related_pathways %}
<!-- Pathways -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-pathway-link"
data-toggle="collapse"
data-parent="#reaction-detail"
href="#reaction-pathway"
>Pathways</a
>
</h4>
</div>
<div id="reaction-pathway" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for r in reaction.related_pathways %}
<a class="list-group-item" href="{{ r.url }}"
>{{ r.name|safe }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if reaction.scenarios.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-scenario-link"
data-toggle="collapse"
data-parent="#reaction-detail"
href="#reaction-scenario"
>Scenarios</a
>
</h4>
</div>
<div id="reaction-scenario" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for s in reaction.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}"
>{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a
>
{% endfor %}
</div>
</div>
{% endif %}
<!-- External Identifiers -->
{% if reaction.get_external_identifiers %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-external-identifier-link"
data-toggle="collapse"
data-parent="#reaction-detail"
href="#reaction-external-identifier"
>External Identifier</a
>
</h4>
</div>
<div
id="reaction-external-identifier"
class="panel-collapse in collapse"
>
<div class="panel-body list-group-item">
{% if reaction.get_rhea_identifiers %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-rhea-identifier-link"
data-toggle="collapse"
data-parent="#reaction-external-identifier"
href="#reaction-rhea-identifier"
>Rhea</a
>
</h4>
</div>
<div
id="reaction-rhea-identifier"
class="panel-collapse in collapse"
>
{% for eid in reaction.get_rhea_identifiers %}
<a class="list-group-item" href="{{ eid.external_url }}"
>{{ eid.identifier_value }}</a
>
{% endfor %}
</div>
{% endif %}
{% if reaction.get_uniprot_identifiers %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="reaction-uniprot-identifier-link"
data-toggle="collapse"
data-parent="#reaction-external-identifier"
href="#reaction-uniprot-identifier"
>UniProt</a
>
</h4>
</div>
<div
id="reaction-uniprot-identifier"
class="panel-collapse in collapse"
>
{% for eid in reaction.get_uniprot_identifiers %}
<a class="list-group-item" href="{{ eid.external_url }}"
>10 SwissProt entries ({{ eid.identifier_value }})</a
>
{% endfor %}
</div>
{% endif %}
</div>
</div>
{% endif %}
</div>
</div>
{% endblock content %}

188
templates/objects/scenario.html
View File

@ -2,88 +2,120 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/add_additional_information_modal.html" %}
{% include "modals/objects/update_scenario_additional_information_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="scenario-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ scenario.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/scenario.html" %}
{% endblock %}
</ul>
</div>
</div>
</div>
</div>
{% block action_modals %}
{% include "modals/objects/add_additional_information_modal.html" %}
{% include "modals/objects/update_scenario_additional_information_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="scenario-detail">
<div class="panel panel-default">
<div class="panel-heading">Description</div>
<div class="panel-body">
{{ scenario.description|safe }}
<br>
{{ scenario.scenario_type }}
<br>
Reported {{ scenario.scenario_date }}
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ scenario.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/scenario.html" %}
{% endblock %}
</ul>
</div>
</div>
</div>
</div>
<div class="table-responsive">
<table id="scenario-table" class="table table-bordered table-striped table-hover">
<tbody>
<tr>
<th>Property</th>
<th>Value</th>
<th>Unit</th>
{% if meta.can_edit %}
<th>Remove</th>
{% endif %}
</tr>
<div class="panel panel-default">
<div class="panel-heading">Description</div>
<div class="panel-body">
{{ scenario.description|safe }}
<br />
{{ scenario.scenario_type }}
<br />
Reported {{ scenario.scenario_date }}
</div>
</div>
{% for ai in scenario.get_additional_information %}
<tr>
<td> {{ ai.property_name|safe }} </td>
<td> {{ ai.property_data|safe }} </td>
<td> {{ ai.property_unit|safe }} </td>
{% if meta.can_edit %}
<td>
<form action="{% url 'package scenario detail' scenario.package.uuid scenario.uuid %}" method="post">
{% csrf_token %}
<input type="hidden" name="uuid" value="{{ ai.uuid }}">
<input type="hidden" name="hidden" value="delete-additional-information">
<button type="submit" class="btn"><span class="glyphicon glyphicon-minus"></span></button>
</form>
</td>
{% endif %}
</tr>
{% endfor %}
<div class="table-responsive">
<table
id="scenario-table"
class="table-bordered table-striped table-hover table"
>
<tbody>
<tr>
<th>Property</th>
<th>Value</th>
<th>Unit</th>
{% if meta.can_edit %}
<th>Remove</th>
{% endif %}
</tr>
{% for ai in scenario.get_additional_information %}
<tr>
<td>{{ ai.property_name|safe }}</td>
<td>{{ ai.property_data|safe }}</td>
<td>{{ ai.property_unit|safe }}</td>
{% if meta.can_edit %}
<tr>
<td></td>
<td></td>
<td>Delete all</td>
<td>
<form action="{% url 'package scenario detail' scenario.package.uuid scenario.uuid %}" method="post">
{% csrf_token %}
<input type="hidden" name="hidden" value="delete-all-additional-information">
<button type="submit" class="btn"><span class="glyphicon glyphicon-trash"></span></button>
</form>
</td>
</tr>
<td>
<form
action="{% url 'package scenario detail' scenario.package.uuid scenario.uuid %}"
method="post"
>
{% csrf_token %}
<input type="hidden" name="uuid" value="{{ ai.uuid }}" />
<input
type="hidden"
name="hidden"
value="delete-additional-information"
/>
<button type="submit" class="btn">
<span class="glyphicon glyphicon-minus"></span>
</button>
</form>
</td>
{% endif %}
</tbody>
</table>
</div>
{% endblock content %}
</tr>
{% endfor %}
{% if meta.can_edit %}
<tr>
<td></td>
<td></td>
<td>Delete all</td>
<td>
<form
action="{% url 'package scenario detail' scenario.package.uuid scenario.uuid %}"
method="post"
>
{% csrf_token %}
<input
type="hidden"
name="hidden"
value="delete-all-additional-information"
/>
<button type="submit" class="btn">
<span class="glyphicon glyphicon-trash"></span>
</button>
</form>
</td>
</tr>
{% endif %}
</tbody>
</table>
</div>
{% endblock content %}

595
templates/objects/simple_rule.html
View File

@ -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 %}

302
templates/objects/user.html
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@ -2,157 +2,195 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/edit_user_modal.html" %}
{% include "modals/objects/edit_password_modal.html" %}
{% include "modals/collections/new_prediction_setting_modal.html" %}
{% include "modals/objects/manage_api_token_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
{% block action_modals %}
{% include "modals/objects/edit_user_modal.html" %}
{% include "modals/objects/edit_password_modal.html" %}
{% include "modals/collections/new_prediction_setting_modal.html" %}
{% include "modals/objects/manage_api_token_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="user-detail">
<div class="panel-group" id="user-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ user.username }}
<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/user.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
<p> On this page you can modify your account or set preferences such as prediction settings.</p>
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ user.username }}
<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/user.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
<p>
On this page you can modify your account or set preferences such as
prediction settings.
</p>
</div>
</div>
<!-- Default Package -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="default-package-link" data-toggle="collapse" data-parent="#user-detail"
href="#default-package">Default Package</a>
</h4>
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="default-package-link"
data-toggle="collapse"
data-parent="#user-detail"
href="#default-package"
>Default Package</a
>
</h4>
</div>
<div id="default-package" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<li class="list-group-item">
<a href="{{ user.default_package.url }}"> {{ user.default_package.name|safe }}</a>
</li>
</div>
<div id="default-package" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<li class="list-group-item">
<a href="{{ user.default_package.url }}">
{{ user.default_package.name|safe }}</a
>
</li>
</div>
</div>
<!-- Groups -->
{% if meta.available_groups|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="group-links" data-toggle="collapse" data-parent="#user-detail"
href="#groups">Groups</a>
<a
id="group-links"
data-toggle="collapse"
data-parent="#user-detail"
href="#groups"
>Groups</a
>
</h4>
</div>
<div id="groups" class="panel-collapse collapse in">
</div>
<div id="groups" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for g in meta.available_groups %}
{% for g in meta.available_groups %}
<li class="list-group-item">
<a href="{{ g.url }}"> {{ g.name|safe }}</a>
<a href="{{ g.url }}"> {{ g.name|safe }}</a>
</li>
{% endfor %}
{% endfor %}
</div>
</div>
</div>
{% endif %}
<!-- Current Prediction Settings -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="current-prediction-setting-links" data-toggle="collapse" data-parent="#user-detail"
href="#current-prediction-setting">Current Prediction Setting</a>
</h4>
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="current-prediction-setting-links"
data-toggle="collapse"
data-parent="#user-detail"
href="#current-prediction-setting"
>Current Prediction Setting</a
>
</h4>
</div>
<div id="current-prediction-setting" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<table class="table table-bordered table-hover">
<tr style="background-color: rgba(0, 0, 0, 0.08);">
<th scope="col" width="20%">Parameter</th>
<th scope="col" width="80%">Value</th>
</tr>
<tbody>
{% if user.default_setting.model %}
<tr>
<td width="20%">Model</td>
<td width="80%">
<table width="100%" class="table table-bordered table-hover">
<tbody>
<tr>
<td colspan="2">
<li class="list-group-item">
<a href="{{user.default_setting.model.url}}">
{{ user.default_setting.model.name|safe }}
</a>
</li>
</td>
</tr>
<tr>
<th width="20%">Model Parameter</th>
<th width="80%">Parameter Value</th>
</tr>
<tr>
<td width="20%">
Threshold
</td>
<td width="80%">
{{ user.default_setting.model_threshold }}
</td>
</tr>
</tbody>
</table>
</td>
</tr>
{% endif %}
{% if user.default_setting.rule_packages.all %}
<tr>
<td width="20%">Rule Packages</td>
<td width="80%">
<table width="100%" class="table table-bordered table-hover">
<tbody>
<tr>
<td colspan="2">
{% for p in user.default_setting.rule_packages.all %}
<li class="list-group-item">
<a href="{{p.url}}">
{{ p.name|safe }}
</a>
</li>
{% endfor %}
</td>
</tr>
</tbody>
</table>
</td>
</tr>
{% endif %}
<tr>
<td>
<p>Max Nodes</p>
</td>
<td>
<p>{{ user.default_setting.max_nodes }}</p>
</td>
</tr>
<tr>
<td>
<p>Max Depth</p>
</td>
<td>
<p>{{ user.default_setting.max_depth }}</p>
</td>
</tr>
</tbody>
</table>
</div>
<div id="current-prediction-setting" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<table class="table-bordered table-hover table">
<tr style="background-color: rgba(0, 0, 0, 0.08);">
<th scope="col" width="20%">Parameter</th>
<th scope="col" width="80%">Value</th>
</tr>
<tbody>
{% if user.default_setting.model %}
<tr>
<td width="20%">Model</td>
<td width="80%">
<table width="100%" class="table-bordered table-hover table">
<tbody>
<tr>
<td colspan="2">
<li class="list-group-item">
<a href="{{ user.default_setting.model.url }}">
{{ user.default_setting.model.name|safe }}
</a>
</li>
</td>
</tr>
<tr>
<th width="20%">Model Parameter</th>
<th width="80%">Parameter Value</th>
</tr>
<tr>
<td width="20%">Threshold</td>
<td width="80%">
{{ user.default_setting.model_threshold }}
</td>
</tr>
</tbody>
</table>
</td>
</tr>
{% endif %}
{% if user.default_setting.rule_packages.all %}
<tr>
<td width="20%">Rule Packages</td>
<td width="80%">
<table width="100%" class="table-bordered table-hover table">
<tbody>
<tr>
<td colspan="2">
{% for p in user.default_setting.rule_packages.all %}
<li class="list-group-item">
<a href="{{ p.url }}"> {{ p.name|safe }} </a>
</li>
{% endfor %}
</td>
</tr>
</tbody>
</table>
</td>
</tr>
{% endif %}
<tr>
<td>
<p>Max Nodes</p>
</td>
<td>
<p>{{ user.default_setting.max_nodes }}</p>
</td>
</tr>
<tr>
<td>
<p>Max Depth</p>
</td>
<td>
<p>{{ user.default_setting.max_depth }}</p>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
{% endblock content %}