forked from enviPath/enviPy
Merge remote-tracking branch 'origin/develop' into fix/xss
# Conflicts: # templates/modals/collections/new_model_modal.html
This commit is contained in:
Liam Brydon
@ -22,6 +22,10 @@
|
||||
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a>
|
||||
</li>
|
||||
{% if meta.can_edit %}
|
||||
<li>
|
||||
<a class="button" data-toggle="modal" data-target="#identify_missing_rules_modal">
|
||||
<i class="glyphicon glyphicon-question-sign"></i> Identify Missing Rules</a>
|
||||
</li>
|
||||
<li role="separator" class="divider"></li>
|
||||
<li>
|
||||
<a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
|
||||
|
||||
71
templates/collections/joblog.html
Normal file
71
templates/collections/joblog.html
Normal file
@ -0,0 +1,71 @@
|
||||
{% extends "framework.html" %}
|
||||
{% load static %}
|
||||
{% load envipytags %}
|
||||
{% block content %}
|
||||
|
||||
<div class="panel-group" id="reviewListAccordion">
|
||||
<div class="panel panel-default">
|
||||
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
|
||||
Jobs
|
||||
</div>
|
||||
<div class="panel-body">
|
||||
<p>
|
||||
Job Logs Desc
|
||||
</p>
|
||||
|
||||
</div>
|
||||
|
||||
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
|
||||
<h4 class="panel-title">
|
||||
<a id="job-accordion-link" data-toggle="collapse" data-parent="#job-accordion" href="#jobs">
|
||||
Jobs
|
||||
</a>
|
||||
</h4>
|
||||
</div>
|
||||
<div id="jobs"
|
||||
class="panel-collapse collapse in">
|
||||
<div class="panel-body list-group-item" id="job-content">
|
||||
<table class="table table-bordered table-hover">
|
||||
<tr style="background-color: rgba(0, 0, 0, 0.08);">
|
||||
<th scope="col">ID</th>
|
||||
<th scope="col">Name</th>
|
||||
<th scope="col">Status</th>
|
||||
<th scope="col">Queued</th>
|
||||
<th scope="col">Done</th>
|
||||
<th scope="col">Result</th>
|
||||
</tr>
|
||||
<tbody>
|
||||
{% for job in jobs %}
|
||||
<tr>
|
||||
<td>{{ job.task_id }}</td>
|
||||
<td>{{ job.job_name }}</td>
|
||||
<td>{{ job.status }}</td>
|
||||
<td>{{ job.created }}</td>
|
||||
<td>{{ job.done_at }}</td>
|
||||
{% if job.task_result and job.task_result|is_url == True %}
|
||||
<td><a href="{{ job.task_result }}">Result</a></td>
|
||||
{% elif job.task_result %}
|
||||
<td>{{ job.task_result|slice:"40" }}...</td>
|
||||
{% else %}
|
||||
<td>Empty</td>
|
||||
{% endif %}
|
||||
</tr>
|
||||
{% endfor %}
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<!-- Unreviewable objects such as User / Group / Setting -->
|
||||
<ul class='list-group'>
|
||||
{% for obj in objects %}
|
||||
{% if object_type == 'user' %}
|
||||
<a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
|
||||
{% else %}
|
||||
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
{% endblock content %}
|
||||
@ -56,7 +56,7 @@
|
||||
(function () {
|
||||
var u = "//matomo.envipath.com/";
|
||||
_paq.push(['setTrackerUrl', u + 'matomo.php']);
|
||||
_paq.push(['setSiteId', '10']);
|
||||
_paq.push(['setSiteId', '{{ meta.site_id }}']);
|
||||
var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
|
||||
g.async = true;
|
||||
g.src = u + 'matomo.js';
|
||||
@ -227,21 +227,23 @@
|
||||
<div class="row">
|
||||
<div class="col-lg-12">
|
||||
<ul class="nav nav-pills nav-justified">
|
||||
<li><a href="http://eawag.ch" target="_blank">
|
||||
<img id="image-ealogo"
|
||||
height="60"
|
||||
src='{% static "/images/ealogo.gif" %}'
|
||||
alt="Eawag"/>
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="http://ml.auckland.ac.nz" target="_blank">
|
||||
<img id="image-uoalogo"
|
||||
height="60"
|
||||
src='{% static "/images/uoa.png" %}'
|
||||
<img id="image-uoalogo" height="60" src='{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}'
|
||||
alt="The Univserity of Auckland"/>
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://eawag.ch" target="_blank">
|
||||
<img id="image-ealogo" height="60" src='{% static "/images/ealogo.gif" %}' alt="Eawag"/>
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://www.uzh.ch/" target="_blank">
|
||||
<img id="image-ufzlogo" height="60" src='{% static "/images/uzh-logo.svg" %}'
|
||||
alt="University of Zurich"/>
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -19,113 +19,117 @@
|
||||
prediction. You just need to set a name and the packages
|
||||
you want the object to be based on. There are multiple types of models available.
|
||||
For additional information have a look at our
|
||||
<a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki >></a>
|
||||
<a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki
|
||||
>></a>
|
||||
</div>
|
||||
<!-- Name -->
|
||||
<label for="model-name">Name</label>
|
||||
<input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
|
||||
|
||||
<!-- Description -->
|
||||
<label for="model-description">Description</label>
|
||||
<input id="model-description" name="model-description" class="form-control"
|
||||
placeholder="Description"/>
|
||||
|
||||
<!-- Model Type -->
|
||||
<label for="model-type">Model Type</label>
|
||||
<select id="model-type" name="model-type" class="form-control" data-width='100%'>
|
||||
<option disabled selected>Select Model Type</option>
|
||||
{% for k, v in model_types.items %}
|
||||
<option value="{{ v }}">{{ k }}</option>
|
||||
<option value="{{ v }}">{{ k }}</option>
|
||||
{% endfor %}
|
||||
</select>
|
||||
<!-- ML and Rule Based Based Form-->
|
||||
<div id="package-based-relative-reasoning-specific-form">
|
||||
<!-- Rule Packages -->
|
||||
<label for="package-based-relative-reasoning-rule-packages">Rule Packages</label>
|
||||
<select id="package-based-relative-reasoning-rule-packages" name="package-based-relative-reasoning-rule-packages"
|
||||
data-actions-box='true' class="form-control" multiple data-width='100%'>
|
||||
|
||||
<!-- Rule Packages -->
|
||||
<div id="rule-packages" class="ep-model-param mlrr rbrr">
|
||||
<label for="model-rule-packages">Rule Packages</label>
|
||||
<select id="model-rule-packages" name="model-rule-packages" data-actions-box='true'
|
||||
class="form-control" multiple data-width='100%'>
|
||||
<option disabled>Reviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
||||
{% endif %}
|
||||
{% if obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
|
||||
<option disabled>Unreviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if not obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
||||
{% endif %}
|
||||
{% if not obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
</select>
|
||||
<!-- Data Packages -->
|
||||
<label for="package-based-relative-reasoning-data-packages" >Data Packages</label>
|
||||
<select id="package-based-relative-reasoning-data-packages" name="package-based-relative-reasoning-data-packages"
|
||||
data-actions-box='true' class="form-control" multiple data-width='100%'>
|
||||
<option disabled>Reviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
|
||||
<option disabled>Unreviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if not obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
</select>
|
||||
|
||||
<div id="ml-relative-reasoning-specific-form">
|
||||
<!-- Fingerprinter -->
|
||||
<label for="ml-relative-reasoning-fingerprinter">Fingerprinter</label>
|
||||
<select id="ml-relative-reasoning-fingerprinter" name="ml-relative-reasoning-fingerprinter"
|
||||
class="form-control">
|
||||
<option value="MACCS" selected>MACCS Fingerprinter</option>
|
||||
</select>
|
||||
{% if meta.enabled_features.PLUGINS and additional_descriptors %}
|
||||
<!-- Property Plugins go here -->
|
||||
<label for="ml-relative-reasoning-additional-fingerprinter">Additional Fingerprinter /
|
||||
Descriptors</label>
|
||||
<select id="ml-relative-reasoning-additional-fingerprinter"
|
||||
name="ml-relative-reasoning-additional-fingerprinter" class="form-control">
|
||||
<option disabled selected>Select Additional Fingerprinter / Descriptor</option>
|
||||
{% for k, v in additional_descriptors.items %}
|
||||
<option value="{{ v }}">{{ k }}</option>
|
||||
{% endfor %}
|
||||
</select>
|
||||
{% endif %}
|
||||
|
||||
<label for="ml-relative-reasoning-threshold">Threshold</label>
|
||||
<input type="number" min="0" max="1" step="0.05" value="0.5"
|
||||
id="ml-relative-reasoning-threshold"
|
||||
name="ml-relative-reasoning-threshold" class="form-control">
|
||||
</div>
|
||||
{% if meta.enabled_features.APPLICABILITY_DOMAIN %}
|
||||
<!-- Build AD? -->
|
||||
<div class="checkbox">
|
||||
<label>
|
||||
<input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
|
||||
Applicability Domain?
|
||||
</label>
|
||||
</div>
|
||||
<div id="ad-params" style="display:none">
|
||||
<!-- Num Neighbors -->
|
||||
<label for="num-neighbors">Number of Neighbors</label>
|
||||
<input id="num-neighbors" name="num-neighbors" type="number" class="form-control" value="5"
|
||||
step="1" min="0" max="10">
|
||||
<!-- Local Compatibility -->
|
||||
<label for="local-compatibility-threshold">Local Compatibility Threshold</label>
|
||||
<input id="local-compatibility-threshold" name="local-compatibility-threshold" type="number"
|
||||
class="form-control" value="0.5" step="0.01" min="0" max="1">
|
||||
<!-- Reliability -->
|
||||
<label for="reliability-threshold">Reliability Threshold</label>
|
||||
<input id="reliability-threshold" name="reliability-threshold" type="number"
|
||||
class="form-control" value="0.5" step="0.01" min="0" max="1">
|
||||
</div>
|
||||
{% endif %}
|
||||
</div>
|
||||
<!-- EnviFormer-->
|
||||
<div id="enviformer-specific-form">
|
||||
<label for="enviformer-threshold">Threshold</label>
|
||||
<input type="number" min="0" max="1" step="0.05" value="0.5" id="enviformer-threshold"
|
||||
name="enviformer-threshold" class="form-control">
|
||||
|
||||
<!-- Data Packages -->
|
||||
<div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
|
||||
<label for="model-data-packages">Data Packages</label>
|
||||
<select id="model-data-packages" name="model-data-packages" data-actions-box='true'
|
||||
class="form-control" multiple data-width='100%'>
|
||||
<option disabled>Reviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
|
||||
<option disabled>Unreviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if not obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
</select>
|
||||
</div>
|
||||
|
||||
<!-- Fingerprinter -->
|
||||
<div id="fingerprinter" class="ep-model-param mlrr">
|
||||
<label for="model-fingerprinter">Fingerprinter</label>
|
||||
<select id="model-fingerprinter" name="model-fingerprinter" data-actions-box='true'
|
||||
class="form-control" multiple data-width='100%'>
|
||||
<option value="MACCS" selected>MACCS Fingerprinter</option>
|
||||
{% if meta.enabled_features.PLUGINS and additional_descriptors %}
|
||||
<option disabled selected>Select Additional Fingerprinter / Descriptor</option>
|
||||
{% for k, v in additional_descriptors.items %}
|
||||
<option value="{{ v }}">{{ k }}</option>
|
||||
{% endfor %}
|
||||
{% endif %}
|
||||
</select>
|
||||
</div>
|
||||
|
||||
<!-- Threshold -->
|
||||
<div id="threshold" class="ep-model-param mlrr enviformer">
|
||||
<label for="model-threshold">Threshold</label>
|
||||
<input type="number" min="0" max="1" step="0.05" value="0.5" id="model-threshold"
|
||||
name="model-threshold" class="form-control">
|
||||
</div>
|
||||
|
||||
<div id="appdomain" class="ep-model-param mlrr">
|
||||
{% if meta.enabled_features.APPLICABILITY_DOMAIN %}
|
||||
<!-- Build AD? -->
|
||||
<div class="checkbox">
|
||||
<label>
|
||||
<input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
|
||||
Applicability Domain?
|
||||
</label>
|
||||
</div>
|
||||
<div id="ad-params" style="display:none">
|
||||
<!-- Num Neighbors -->
|
||||
<label for="num-neighbors">Number of Neighbors</label>
|
||||
<input id="num-neighbors" name="num-neighbors" type="number" class="form-control"
|
||||
value="5"
|
||||
step="1" min="0" max="10">
|
||||
<!-- Local Compatibility -->
|
||||
<label for="local-compatibility-threshold">Local Compatibility Threshold</label>
|
||||
<input id="local-compatibility-threshold" name="local-compatibility-threshold"
|
||||
type="number"
|
||||
class="form-control" value="0.5" step="0.01" min="0" max="1">
|
||||
<!-- Reliability -->
|
||||
<label for="reliability-threshold">Reliability Threshold</label>
|
||||
<input id="reliability-threshold" name="reliability-threshold" type="number"
|
||||
class="form-control" value="0.5" step="0.01" min="0" max="1">
|
||||
</div>
|
||||
{% endif %}
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
@ -138,53 +142,47 @@
|
||||
</div>
|
||||
|
||||
<script>
|
||||
$(function() {
|
||||
// Initially hide all "specific" forms
|
||||
$("div[id$='-specific-form']").each( function() {
|
||||
$(this).hide();
|
||||
});
|
||||
$(function () {
|
||||
// Built in Model Types
|
||||
var nativeModelTypes = [
|
||||
"mlrr",
|
||||
"rbrr",
|
||||
"enviformer",
|
||||
]
|
||||
|
||||
$('#model-type').selectpicker();
|
||||
$("#ml-relative-reasoning-fingerprinter").selectpicker();
|
||||
$("#package-based-relative-reasoning-rule-packages").selectpicker();
|
||||
$("#package-based-relative-reasoning-data-packages").selectpicker();
|
||||
$("#package-based-relative-reasoning-evaluation-packages").selectpicker();
|
||||
if ($('#ml-relative-reasoning-additional-fingerprinter').length > 0) {
|
||||
$("#ml-relative-reasoning-additional-fingerprinter").selectpicker();
|
||||
}
|
||||
|
||||
$("#build-app-domain").change(function () {
|
||||
if ($(this).is(":checked")) {
|
||||
$('#ad-params').show();
|
||||
} else {
|
||||
$('#ad-params').hide();
|
||||
}
|
||||
});
|
||||
|
||||
// On change hide all and show only selected
|
||||
$("#model-type").change(function() {
|
||||
$("div[id$='-specific-form']").each( function() {
|
||||
// Initially hide all "specific" forms
|
||||
$(".ep-model-param").each(function () {
|
||||
$(this).hide();
|
||||
});
|
||||
val = $('option:selected', this).val();
|
||||
|
||||
if (val === 'ml-relative-reasoning' || val === 'rule-based-relative-reasoning') {
|
||||
$("#package-based-relative-reasoning-specific-form").show();
|
||||
if (val === 'ml-relative-reasoning') {
|
||||
$("#ml-relative-reasoning-specific-form").show();
|
||||
$('#model-type').selectpicker();
|
||||
$("#model-fingerprinter").selectpicker();
|
||||
$("#model-rule-packages").selectpicker();
|
||||
$("#model-data-packages").selectpicker();
|
||||
|
||||
$("#build-app-domain").change(function () {
|
||||
if ($(this).is(":checked")) {
|
||||
$('#ad-params').show();
|
||||
} else {
|
||||
$('#ad-params').hide();
|
||||
}
|
||||
} else {
|
||||
$("#" + val + "-specific-form").show();
|
||||
}
|
||||
});
|
||||
|
||||
// On change hide all and show only selected
|
||||
$("#model-type").change(function () {
|
||||
$('.ep-model-param').hide();
|
||||
var modelType = $('#model-type').val();
|
||||
if (nativeModelTypes.indexOf(modelType) !== -1) {
|
||||
$('.' + modelType).show();
|
||||
} else {
|
||||
// do nothing
|
||||
}
|
||||
});
|
||||
|
||||
$('#new_model_modal_form_submit').on('click', function (e) {
|
||||
e.preventDefault();
|
||||
$('#new_model_form').submit();
|
||||
});
|
||||
|
||||
});
|
||||
|
||||
$('#new_model_modal_form_submit').on('click', function(e){
|
||||
e.preventDefault();
|
||||
$('#new_model_form').submit();
|
||||
});
|
||||
|
||||
});
|
||||
|
||||
|
||||
|
||||
</script>
|
||||
|
||||
@ -18,10 +18,10 @@
|
||||
For evaluation, you need to select the packages you want to use.
|
||||
While the model is evaluating, you can use the model for predictions.
|
||||
</div>
|
||||
<!-- Evaluation -->
|
||||
<label for="relative-reasoning-evaluation-packages">Evaluation Packages</label>
|
||||
<select id="relative-reasoning-evaluation-packages" name=relative-reasoning-evaluation-packages"
|
||||
data-actions-box='true' class="form-control" multiple data-width='100%'>
|
||||
<!-- Evaluation Packages -->
|
||||
<label for="model-evaluation-packages">Evaluation Packages</label>
|
||||
<select id="model-evaluation-packages" name="model-evaluation-packages" data-actions-box='true'
|
||||
class="form-control" multiple data-width='100%'>
|
||||
<option disabled>Reviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if obj.reviewed %}
|
||||
@ -36,7 +36,16 @@
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
</select>
|
||||
<input type="hidden" name="hidden" value="evaluate">
|
||||
|
||||
<!-- Eval Type -->
|
||||
<label for="model-evaluation-type">Evaluation Type</label>
|
||||
<select id="model-evaluation-type" name="model-evaluation-type" class="form-control">
|
||||
<option disabled selected>Select evaluation type</option>
|
||||
<option value="sg">Single Generation</option>
|
||||
<option value="mg">Multiple Generations</option>
|
||||
</select>
|
||||
|
||||
<input type="hidden" name="hidden" value="evaluate">
|
||||
</form>
|
||||
</div>
|
||||
<div class="modal-footer">
|
||||
@ -51,7 +60,7 @@
|
||||
|
||||
$(function () {
|
||||
|
||||
$("#relative-reasoning-evaluation-packages").selectpicker();
|
||||
$("#model-evaluation-packages").selectpicker();
|
||||
|
||||
$('#evaluate_model_form_submit').on('click', function (e) {
|
||||
e.preventDefault();
|
||||
|
||||
@ -19,6 +19,7 @@
|
||||
<select id="scenario-select" name="selected-scenarios" data-actions-box='true' class="form-control"
|
||||
multiple data-width='100%'>
|
||||
<option disabled>Select Scenarios</option>
|
||||
<option value="" hidden></option>
|
||||
</select>
|
||||
</form>
|
||||
</div>
|
||||
@ -66,7 +67,7 @@
|
||||
$('#set_scenario_modal_form_submit').on('click', function (e) {
|
||||
e.preventDefault();
|
||||
if ($('#scenario-select').val().length == 0) {
|
||||
$('#scenario-select').val([''])
|
||||
$('#scenario-select').val("")
|
||||
}
|
||||
$('#set_scenario_modal_form').submit();
|
||||
});
|
||||
|
||||
54
templates/modals/objects/identify_missing_rules_modal.html
Normal file
54
templates/modals/objects/identify_missing_rules_modal.html
Normal file
@ -0,0 +1,54 @@
|
||||
{% load static %}
|
||||
<!-- Identify Missing Rules -->
|
||||
<div id="identify_missing_rules_modal" class="modal" tabindex="-1">
|
||||
<div class="modal-dialog">
|
||||
<div class="modal-content">
|
||||
<div class="modal-header">
|
||||
<h3 class="modal-title">Identify Missing Rules</h3>
|
||||
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
|
||||
<span aria-hidden="true">×</span>
|
||||
</button>
|
||||
</div>
|
||||
<div class="modal-body">
|
||||
By clicking on Download we'll search the Pathway for Reactions that are not backed by
|
||||
a Rule or which can be assembled by chaining two rules.
|
||||
<form id="identify-missing-rules-modal-form" accept-charset="UTF-8" action="{{ pathway.url }}"
|
||||
data-remote="true" method="GET">
|
||||
<label for="rule-package">Select the Rule Package</label>
|
||||
<select id="rule-package" name="rule-package" data-actions-box='true' class="form-control"
|
||||
data-width='100%'>
|
||||
<option disabled>Reviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name }}</option>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
|
||||
<option disabled>Unreviewed Packages</option>
|
||||
{% for obj in meta.readable_packages %}
|
||||
{% if not obj.reviewed %}
|
||||
<option value="{{ obj.url }}">{{ obj.name }}</option>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
</select>
|
||||
<input type="hidden" name="identify-missing-rules" value="true"/>
|
||||
</form>
|
||||
</div>
|
||||
<div class="modal-footer">
|
||||
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
|
||||
<button type="button" class="btn btn-primary" id="identify-missing-rules-modal-submit">Download</button>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<script>
|
||||
$(function () {
|
||||
|
||||
$('#identify-missing-rules-modal-submit').click(function (e) {
|
||||
e.preventDefault();
|
||||
$('#identify-missing-rules-modal-form').submit();
|
||||
$('#identify_missing_rules_modal').modal('hide');
|
||||
});
|
||||
|
||||
})
|
||||
</script>
|
||||
@ -88,19 +88,41 @@
|
||||
</div>
|
||||
{% endif %}
|
||||
|
||||
<!-- 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">
|
||||
<div class="panel-body list-group-item">
|
||||
|
||||
{% 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>
|
||||
|
||||
<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>
|
||||
</div>
|
||||
{% endblock content %}
|
||||
|
||||
@ -184,7 +184,7 @@
|
||||
</div>
|
||||
<div id="compound-external-identifier" class="panel-collapse collapse in">
|
||||
<div class="panel-body list-group-item">
|
||||
{% if compound.get_pubchem_identifiers %}
|
||||
{% if compound.get_pubchem_compound_identifiers %}
|
||||
<div class="panel panel-default panel-heading list-group-item"
|
||||
style="background-color:silver">
|
||||
<h4 class="panel-title">
|
||||
@ -194,12 +194,28 @@
|
||||
</h4>
|
||||
</div>
|
||||
<div id="compound-pubchem-identifier" class="panel-collapse collapse in">
|
||||
{% for eid in compound.get_pubchem_identifiers %}
|
||||
{% 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">
|
||||
|
||||
105
templates/objects/enzymelink.html
Normal file
105
templates/objects/enzymelink.html
Normal file
@ -0,0 +1,105 @@
|
||||
{% 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>
|
||||
|
||||
<!-- 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 }}. <a
|
||||
href="https://wiki.envipath.org/index.php/Rules#EnzymeLinks" target="#">Learn more >></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>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
{% endblock content %}
|
||||
@ -117,7 +117,7 @@
|
||||
<!-- End Predict Panel -->
|
||||
{% endif %}
|
||||
|
||||
{% if model.app_domain %}
|
||||
{% if model.ready_for_prediction and model.app_domain %}
|
||||
<!-- App Domain -->
|
||||
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
|
||||
<h4 class="panel-title">
|
||||
|
||||
@ -84,6 +84,7 @@
|
||||
{% 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" %}
|
||||
@ -178,9 +179,6 @@
|
||||
</nav>
|
||||
<div id="vizdiv" >
|
||||
<svg id="pwsvg">
|
||||
{% if debug %}
|
||||
<rect width="100%" height="100%" fill="aliceblue"/>
|
||||
{% endif %}
|
||||
<defs>
|
||||
<marker id="arrow" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
|
||||
orient="auto-start-reverse" markerUnits="userSpaceOnUse">
|
||||
|
||||
@ -125,6 +125,23 @@
|
||||
</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">
|
||||
|
||||
@ -202,6 +202,43 @@
|
||||
</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>
|
||||
</div>
|
||||
{% endblock content %}
|
||||
|
||||
Reference in New Issue
Block a user