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Basic System (#31)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#31
This commit is contained in:
jebus
2025-07-23 06:47:07 +12:00
parent 49e02ed97d
commit df896878f1
75 changed files with 3821 additions and 1429 deletions
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126
templates/modals/objects/add_pathway_edge_modal.html Normal file
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{% load static %}
<div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
aria-modal="true"
role="dialog">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
<h4 class="modal-title">Add a Reaction</h4>
</div>
<div class="modal-body">
<form id="add_pathway_edge_modal_form" accept-charset="UTF-8"
action="{% url 'package pathway edge list' meta.current_package.uuid pathway.uuid %}"
data-remote="true" method="post">
{% csrf_token %}
<label for="edge-name">Name</label>
<input id="edge-name" class="form-control" name="edge-name" placeholder="Name"/>
<label for="edge-description">Description</label>
<input id="edge-description" class="form-control" name="edge-description" placeholder="Description"/>
<p></p>
<div class="row">
<div class="col-xs-5">
<legend>Substrate(s)</legend>
</div>
<div class="col-xs-2">
</div>
<div class="col-xs-5">
<legend>Product(s)</legend>
</div>
</div>
<div class="row">
<div class="col-xs-5">
<select id="add_pathway_edge_substrates" name="edge-substrates"
data-actions-box='true' class="form-control" multiple data-width='100%'>
{% for n in pathway.nodes %}
<option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
{% endfor %}
</select>
</div>
<div class="col-xs-2" style="display: flex; justify-content: center; align-items: center;">
<i class="glyphicon glyphicon-arrow-right"></i>
</div>
<div class="col-xs-5">
<select id="add_pathway_edge_products" name="edge-products"
data-actions-box='true' class="form-control" multiple data-width='100%'>
{% for n in pathway.nodes %}
<option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
{% endfor %}
</select>
</div>
</div>
<div class="row">
<p></p>
<div class="col-xs-12" id="reaction_image">
</div>
</div>
</form>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
</button>
<button type="button" class="btn btn-primary" id="add_pathway_edge_modal_form_submit">Submit</button>
</div>
</div>
</div>
</div>
<script>
function reactionImage() {
var substrates = [];
$('#add_pathway_edge_substrates option:selected').each(function () {
var smiles = $(this).data('smiles'); // read data-smiles attribute
substrates.push(smiles);
});
var products = []
$('#add_pathway_edge_products option:selected').each(function () {
var smiles = $(this).data('smiles'); // read data-smiles attribute
products.push(smiles);
});
if (substrates.length > 0 && products.length > 0) {
reaction = substrates.join('.') + ">>" + products.join('.');
$('#reaction_image').empty();
$('#reaction_image').append(
"<img width='100%' src='{% url 'depict' %}?smirks=" + encodeURIComponent(reaction) +"'>"
);
}
}
$(function () {
$("#add_pathway_edge_substrates").selectpicker();
$("#add_pathway_edge_products").selectpicker();
$("#add_pathway_edge_substrates").on('change', function (e) {
reactionImage();
})
$("#add_pathway_edge_products").on('change', function (e) {
reactionImage();
})
$(function () {
$('#add_pathway_edge_modal_form_submit').on('click', function (e) {
e.preventDefault();
$(this).prop("disabled", true);
// submit form
$('#add_pathway_edge_modal_form').submit();
});
});
});
</script>

78
templates/modals/objects/add_pathway_node_modal.html Normal file
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{% load static %}
<div class="modal fade bs-modal-lg" id="add_pathway_node_modal" tabindex="-1" aria-labelledby="add_pathway_node_modal" aria-modal="true"
role="dialog">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
<h4 class="modal-title">Add a Node</h4>
</div>
<div class="modal-body">
<form id="add_pathway_node_modal_form" accept-charset="UTF-8" action="{% url 'package pathway node list' meta.current_package.uuid pathway.uuid %}" data-remote="true" method="post">
{% csrf_token %}
<label for="node-name">Name</label>
<input id="node-name" class="form-control" name="node-name" placeholder="Name"/>
<label for="node-description">Description</label>
<input id="node-description" class="form-control" name="node-description" placeholder="Description"/>
<label for="node-smiles">SMILES</label>
<input type="text" class="form-control" name="node-smiles" placeholder="SMILES" id="node-smiles">
<p></p>
<div>
<iframe id="add_node_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
height="510"></iframe>
</div>
<p></p>
</form>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
</button>
<button type="button" class="btn btn-primary" id="add_pathway_node_modal_form_submit">Submit</button>
</div>
</div>
</div>
</div>
<script>
function newStructureModalketcherToNewStructureModalTextInput() {
$('#node-smiles').val(this.ketcher.getSmiles());
}
$(function() {
$('#add_node_ketcher').on('load', function() {
const checkKetcherReady = () => {
win = this.contentWindow
if (win.ketcher && 'editor' in win.ketcher) {
win.ketcher.editor.event.change.handlers.push({
once: false,
priority: 0,
f: newStructureModalketcherToNewStructureModalTextInput,
ketcher: win.ketcher
});
} else {
setTimeout(checkKetcherReady, 100);
}
};
checkKetcherReady();
})
$(function() {
$('#add_pathway_node_modal_form_submit').on('click', function(e) {
e.preventDefault();
$(this).prop("disabled",true);
// submit form
$('#add_pathway_node_modal_form').submit();
});
});
});
</script>

35
templates/modals/objects/delete_model_modal.html Normal file
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{% load static %}
<!-- Delete Model -->
<div id="delete_model_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Model</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
Deletes the Model.
<form id="delete-model-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" id="hidden" name="hidden" value="delete-model"/>
</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="delete-model-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function () {
$('#delete-model-modal-submit').click(function (e) {
e.preventDefault();
$('#delete-model-modal-form').submit();
});
})
</script>

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templates/modals/objects/delete_node_modal.html Normal file
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{% load static %}
<!-- Delete Node -->
<div id="delete_node_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Node</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
Deletes the Node as well as ingoing and outgoing edges.
<form id="delete-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" id="hidden" name="hidden" value="delete-node"/>
</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="delete-node-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function () {
$('#delete-node-modal-submit').click(function (e) {
e.preventDefault();
$('#delete-node-modal-form').submit();
});
})
</script>

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templates/modals/objects/delete_pathway_edge_modal.html Normal file
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{% load static %}
<!-- Delete Edge -->
<div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Edge</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
Deletes the Edge. Nodes referenced by this edge will remain.
<p></p>
<form id="delete-pathway-edge-modal-form" accept-charset="UTF-8" action="" data-remote="true"
method="post">
{% csrf_token %}
<select id="delete_pathway_edge_edges" name="edge-url"
data-actions-box='true' class="form-control" data-width='100%'>
<option value="" disabled selected>Select Reaction to delete</option>
{% for e in pathway.edges %}
<option value="{{ e.url }}">{{ e.edge_label.name }}</option>
{% endfor %}
</select>
<input type="hidden" id="hidden" name="hidden" value="delete-edge"/>
</form>
<p></p>
<div id="delete_pathway_edge_image"></div>
</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="delete-pathway-edge-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function () {
$("#delete_pathway_edge_edges").selectpicker();
$("#delete_pathway_edge_edges").on('change', function (e) {
edge_url = $('#delete_pathway_edge_edges option:selected').val()
if (edge_url !== "") {
$('#delete_pathway_edge_image').empty();
$('#delete_pathway_edge_image').append(
"<img width='100%' src='" + edge_url + "?image=svg'>"
);
}
})
$('#delete-pathway-edge-modal-submit').click(function (e) {
e.preventDefault();
edge_url = $('#delete_pathway_edge_edges option:selected').val()
if (edge_url === "") {
return;
}
$('#delete-pathway-edge-modal-form').attr('action', edge_url)
$('#delete-pathway-edge-modal-form').submit();
});
})
</script>

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templates/modals/objects/delete_pathway_modal.html Normal file
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{% load static %}
<!-- Delete Pathway -->
<div id="delete_pathway_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Pathway</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
Deletes the Pathway together with all Nodes and Edges.
<form id="delete-pathway-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" id="hidden" name="hidden" value="delete-pathway"/>
</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="delete-pathway-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function () {
$('#delete-pathway-modal-submit').click(function (e) {
e.preventDefault();
$('#delete-pathway-modal-form').submit();
});
})
</script>

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templates/modals/objects/delete_pathway_node_modal.html Normal file
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{% load static %}
<!-- Delete Node -->
<div id="delete_pathway_node_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Node</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
Deletes the Node. Edges having this Node as Substrate or Product will be removed as well.
<p></p>
<form id="delete-pathway-node-modal-form" accept-charset="UTF-8" action="" data-remote="true"
method="post">
{% csrf_token %}
<select id="delete_pathway_node_nodes" name="node-url"
data-actions-box='true' class="form-control" data-width='100%'>
<option value="" disabled selected>Select Compound to delete</option>
{% for n in pathway.nodes %}
<option value="{{ n.url }}">{{ n.default_node_label.name }}</option>
{% endfor %}
</select>
<input type="hidden" id="hidden" name="hidden" value="delete-node"/>
</form>
<p></p>
<div id="delete_pathway_node_image"></div>
</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="delete-pathway-node-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function () {
$("#delete_pathway_node_nodes").selectpicker();
$("#delete_pathway_node_nodes").on('change', function (e) {
node_url = $('#delete_pathway_node_nodes option:selected').val()
if (node_url !== "") {
$('#delete_pathway_node_image').empty();
$('#delete_pathway_node_image').append(
"<img width='100%' src='" + node_url + "?image=svg'>"
);
}
})
$('#delete-pathway-node-modal-submit').click(function (e) {
e.preventDefault();
node_url = $('#delete_pathway_node_nodes option:selected').val()
if (node_url === "") {
return;
}
$('#delete-pathway-node-modal-form').attr('action', node_url)
$('#delete-pathway-node-modal-form').submit();
});
})
</script>

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templates/modals/objects/delete_reaction_modal.html Normal file
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{% load static %}
<!-- Delete Reaction -->
<div id="delete_reaction_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Reaction</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
Deletes the Reaction.
<form id="delete-reaction-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" id="hidden" name="hidden" value="delete-reaction"/>
</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="delete-reaction-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function () {
$('#delete-reaction-modal-submit').click(function (e) {
e.preventDefault();
$('#delete-reaction-modal-form').submit();
});
})
</script>

4
templates/modals/objects/edit_compound_modal.html
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@ -4,13 +4,13 @@
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Create a Compound</h5>
<h5 class="modal-title">Edit Compound</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
<p>Edit a Compound.</p>
<p>Edit Compound.</p>
<form id="edit-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<p>

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templates/modals/objects/edit_node_modal.html Normal file
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{% load static %}
<!-- Edit Node -->
<div id="edit_node_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Edit Node</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
<p>Edit Node.</p>
<form id="edit-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<p>
<label for="node-name">Name</label>
<input id="node-name" class="form-control" name="node-name" value="{{ node.name}}">
</p>
<p>
<label for="node-description">Description</label>
<input id="node-description" type="text" class="form-control"
value="{{ node.description }}"
name="node-description">
</p>
</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="edit-node-modal-submit">Create</button>
</div>
</div>
</div>
</div>
<script>
$(function() {
$('#edit-node-modal-submit').click(function(e){
e.preventDefault();
$('#edit-node-modal-form').submit();
});
});
</script>

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templates/modals/objects/edit_pathway_modal.html Normal file
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{% load static %}
<!-- Edit Pathway -->
<div id="edit_pathway_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Edit Pathway</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
<p>Edit Pathway.</p>
<form id="edit-pathway-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<p>
<label for="pathway-name">Name</label>
<input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name }}">
</p>
<p>
<label for="pathway-description">Description</label>
<textarea id="pathway-description" type="text" class="form-control" name="pathway-description"
rows="10">{{ pathway.description }}</textarea>
</p>
</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="edit-pathway-modal-submit">Update</button>
</div>
</div>
</div>
</div>
<script>
$(function() {
$('#edit-pathway-modal-submit').click(function(e){
e.preventDefault();
$('#edit-pathway-modal-form').submit();
});
})
</script>

1
templates/modals/objects/edit_reaction_modal.html
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@ -10,7 +10,6 @@
<h3 class="modal-title">Update Reaction</h3>
</div>
<div class="modal-body">
<!-- <p>Edit a Reaction.</p>-->
<form id="edit-reaction-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<p>

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templates/modals/objects/edit_rule_modal.html
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{% load static %}
<!-- Edit Rule -->
<div id="edit_rule_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
<h3 class="modal-title">Update Rule</h3>
</div>
<div class="modal-body">
<form id="edit-rule-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<p>
<label for="rule-name">Name</label>
<input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name }}">
</p>
<p>
<label for="rule-description">Description</label>
<input id="rule-description" type="text" class="form-control"
value="{{ rule.description }}" name="rule-description">
</p>
</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="edit-rule-modal-submit">Update</button>
</div>
</div>
</div>
</div>
<script>
$(function() {
$('#edit-rule-modal-submit').click(function(e){
e.preventDefault();
$('#edit-rule-modal-form').submit();
});
});
</script>

1
templates/modals/objects/manage_api_token_modal.html
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@ -70,7 +70,6 @@ $(function() {
e.preventDefault();
const formData = $('#request_api_token_form').serialize();
console.log(formData)
$.post('', formData, function(response) {
$('#new-token-pre').text(response.raw_token);
$('#new-token').show();