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Cleanup (#52)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#52
This commit is contained in:
jebus
2025-08-22 06:36:22 +12:00
parent ec387cc12e
commit 6e6b394289
42 changed files with 222 additions and 368 deletions
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12
epdb/models.py
View File

@ -944,7 +944,7 @@ class SimpleAmbitRule(SimpleRule):
@property
def as_svg(self):
return IndigoUtils.smirks_to_svg(self.smirks, True)
return IndigoUtils.smirks_to_svg(self.smirks, True, width=800, height=400)
class SimpleRDKitRule(SimpleRule):
@ -1203,6 +1203,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
for n in self.root_nodes:
queue.append(n)
# Add unconnected nodes
for n in self.nodes:
if len(n.out_edges.all()) == 0:
if n not in queue:
queue.append(n)
while len(queue):
current = queue.pop()
processed.add(current)
@ -1341,12 +1347,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
pw = Pathway()
pw.package = package
if name is None:
if name is None or name.strip() == '':
name = f"Pathway {Pathway.objects.filter(package=package).count() + 1}"
pw.name = name
if description is not None:
if description is not None and description.strip() != '':
pw.description = description
pw.save()

79
epdb/views.py
View File

@ -4,6 +4,9 @@ from typing import List, Dict, Any
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.db.models import F, Value
from django.db.models.fields import CharField
from django.db.models.functions import Concat
from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
from django.shortcuts import render, redirect
from django.views.decorators.csrf import csrf_exempt
@ -436,8 +439,16 @@ def scenarios(request):
if request.GET.get('all'):
return JsonResponse({
"objects": [
{"name": pw.name, "url": pw.url, "reviewed": True}
for pw in reviewed_scenario_qs
{"name": s.name, "url": s.full_url, "reviewed": True}
for s in reviewed_scenario_qs.annotate(
full_url=Concat(
Value(s.SERVER_URL + '/package/'),
F("package__uuid"),
Value("/scenario/"),
F("uuid"),
output_field=CharField(),
)
)
]
})
@ -517,6 +528,7 @@ def search(request):
packages = PackageManager.get_reviewed_packages()
search_result = SearchManager.search(packages, searchterm, mode)
return JsonResponse(search_result, safe=False)
context = get_base_context(request)
@ -542,6 +554,7 @@ def search(request):
packages = PackageManager.get_reviewed_packages()
context['search_result'] = SearchManager.search(packages, searchterm, mode)
context['search_result']['searchterm'] = searchterm
return render(request, 'search.html', context)
@ -706,7 +719,7 @@ def package_model(request, package_uuid, model_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-model':
if hidden == 'delete':
current_model.delete()
return redirect(current_package.url + '/model')
else:
@ -757,7 +770,7 @@ def package(request, package_uuid):
logger.debug(f"{k}\t{v}")
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-package':
if hidden == 'delete':
logger.debug(current_package.delete())
return redirect(s.SERVER_URL + '/package')
else:
@ -897,7 +910,7 @@ def package_compound(request, package_uuid, compound_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-compound':
if hidden == 'delete':
current_compound.delete()
return redirect(current_package.url + '/compound')
else:
@ -940,6 +953,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
context['meta']['current_package'] = current_package
context['object_type'] = 'structure'
context['breadcrumbs'] = breadcrumbs(current_package, 'compound', current_compound, 'structure')
reviewed_compound_structure_qs = CompoundStructure.objects.none()
unreviewed_compound_structure_qs = CompoundStructure.objects.none()
@ -979,15 +993,38 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
context['title'] = f'enviPath - {current_package.name} - {current_compound.name} - {current_structure.name}'
context['meta']['current_package'] = current_package
context['object_type'] = 'compound'
context['object_type'] = 'structure'
context['compound_structure'] = current_structure
context['current_object'] = current_structure
context['breadcrumbs'] = breadcrumbs(current_package, 'compound', current_compound, 'structure', current_structure)
return render(request, 'objects/compound_structure.html', context)
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete':
# Check if we have to delete the compound as no structure is left
if len(current_structure.compound.structures.all()) == 1:
# This will delete the structure as well
current_compound.delete()
return redirect(current_package.url + '/compound')
else:
if current_structure.normalized_structure:
current_compound.delete()
return redirect(current_package.url + '/compound')
else:
if current_compound.default_structure == current_structure:
current_structure.delete()
current_compound.default_structure = current_compound.structures.all().first()
return redirect(current_compound.url + '/structure')
else:
current_structure.delete()
return redirect(current_compound.url + '/structure')
else:
return HttpResponseBadRequest()
selected_scenarios = request.POST.getlist('selected-scenarios')
if selected_scenarios:
@ -1109,7 +1146,7 @@ def package_rule(request, package_uuid, rule_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-rule':
if hidden == 'delete':
current_rule.delete()
return redirect(current_package.url + '/rule')
else:
@ -1212,7 +1249,7 @@ def package_reaction(request, package_uuid, reaction_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-reaction':
if hidden == 'delete':
current_reaction.delete()
return redirect(current_package.url + '/reaction')
else:
@ -1281,8 +1318,8 @@ def package_pathways(request, package_uuid):
log_post_params(request)
name = request.POST.get('name', 'Pathway ' + str(Pathway.objects.filter(package=current_package).count()))
description = request.POST.get('description', s.DEFAULT_VALUES['description'])
name = request.POST.get('name')
description = request.POST.get('description')
pw_mode = request.POST.get('predict', 'predict')
smiles = request.POST.get('smiles')
@ -1303,7 +1340,14 @@ def package_pathways(request, package_uuid):
return error(request, "Pathway prediction failed!",
f'Pathway prediction failed as received mode "{pw_mode}" is none of {modes}')
prediction_setting = request.POST.get('prediction-setting', None)
if prediction_setting:
prediction_setting = SettingManager.get_setting_by_url(current_user, prediction_setting)
else:
prediction_setting = current_user.prediction_settings()
pw = Pathway.create(current_package, stand_smiles, name=name, description=description)
# set mode
pw.kv.update({'mode': pw_mode})
pw.save()
@ -1316,12 +1360,11 @@ def package_pathways(request, package_uuid):
if pw_mode == 'incremental':
limit = 1
pred_setting = current_user.prediction_settings()
pw.setting = pred_setting
pw.setting = prediction_setting
pw.save()
from .tasks import predict
predict.delay(pw.pk, pred_setting.pk, limit=limit)
predict.delay(pw.pk, prediction_setting.pk, limit=limit)
return redirect(pw.url)
@ -1371,7 +1414,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-pathway':
if hidden == 'delete':
current_pathway.delete()
return redirect(current_package.url + '/pathway')
else:
@ -1514,7 +1557,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
log_post_params(request)
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-node':
if hidden == 'delete':
# pre_delete signal will take care of edge deletion
current_node.delete()
@ -1616,7 +1659,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
'title'] = f'enviPath - {current_package.name} - {current_pathway.name} - {current_edge.edge_label.name}'
context['meta']['current_package'] = current_package
context['object_type'] = 'reaction'
context['object_type'] = 'edge'
context['breadcrumbs'] = breadcrumbs(current_package, 'pathway', current_pathway, 'edge', current_edge)
context['edge'] = current_edge
context['current_object'] = current_edge
@ -1628,7 +1671,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
log_post_params(request)
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-edge':
if hidden == 'delete':
current_edge.delete()
return redirect(current_pathway.url)
@ -1896,7 +1939,7 @@ def group(request, group_uuid):
log_post_params(request)
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-group':
if hidden == 'delete':
current_group.delete()
return redirect(s.SERVER_URL + '/group')
else:

2
templates/actions/objects/compound.html
View File

@ -12,7 +12,7 @@
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#delete_compound_modal">
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
</li>
{% endif %}

2
templates/actions/objects/compound_structure.html
View File

@ -8,7 +8,7 @@
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#delete_compound_structure_modal">
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
</li>
{% endif %}

10
templates/actions/objects/edge.html Normal file
View File

@ -0,0 +1,10 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Edge</a>
</li>
{% endif %}

10
templates/actions/objects/group.html
View File

@ -1,10 +1,10 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#delete_group_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Group</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
<a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
<i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Group</a>
</li>
{% endif %}

2
templates/actions/objects/model.html
View File

@ -1,6 +1,6 @@
{% if meta.can_edit %}
<li>
<a class="button" data-toggle="modal" data-target="#delete_model_modal">
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Model</a>
</li>
{% endif %}

2
templates/actions/objects/node.html
View File

@ -8,7 +8,7 @@
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#delete_node_modal">
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Node</a>
</li>
{% endif %}

2
templates/actions/objects/package.html
View File

@ -12,7 +12,7 @@
<i class="glyphicon glyphicon-duplicate"></i> License</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#delete_package_modal">
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Package</a>
</li>
{% endif %}

2
templates/actions/objects/pathway.html
View File

@ -35,7 +35,7 @@
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#delete_pathway_modal">
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
</li>
{% endif %}

2
templates/actions/objects/reaction.html
View File

@ -8,7 +8,7 @@
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#delete_reaction_modal">
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
</li>
{% endif %}

2
templates/actions/objects/rule.html
View File

@ -8,7 +8,7 @@
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#delete_rule_modal">
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Rule</a>
</li>
{% endif %}

2
templates/actions/objects/user.html
View File

@ -16,7 +16,7 @@
{# <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
{# </li>#}
<li>
<a role="button" data-toggle="modal" data-target="#delete_user_modal">
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Account</a>
</li>
{% endif %}

50
templates/framework.html
View File

@ -83,21 +83,26 @@
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
<ul class="nav navbar-nav navbar-nav-framework">
<li class="dropdown">
<a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>
<ul role="menu" class="dropdown-menu">
<li>
<a class="button" data-toggle="modal" data-target="#predict_modal">
<i class=" glyphicon glyphicon-tag"></i> Predict Pathway
</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#batch_predict_modal">
<i class=" glyphicon glyphicon-tags"></i> Batch Prediction
</a>
</li>
</ul>
<li>
<a class="button" data-toggle="modal" data-target="#predict_modal">
Predict Pathway
</a>
</li>
{# <li class="dropdown">#}
{# <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
{# <ul role="menu" class="dropdown-menu">#}
{# <li>#}
{# <a class="button" data-toggle="modal" data-target="#predict_modal">#}
{# <i class=" glyphicon glyphicon-tag"></i> Predict Pathway#}
{# </a>#}
{# </li>#}
{# <li>#}
{# <a class="button" data-toggle="modal" data-target="#batch_predict_modal">#}
{# <i class=" glyphicon glyphicon-tags"></i> Batch Prediction#}
{# </a>#}
{# </li>#}
{# </ul>#}
{# </li>#}
<li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li>
<li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>
<li><a href="{{ meta.server_url }}/model" id="modelLink">Modelling</a></li>
@ -192,6 +197,23 @@
{% endif %}
{% block content %}
{% endblock content %}
{% if meta.current_package.license %}
<p></p>
<div class="panel-group" id="license_accordion">
<div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
<div class="panel-title">
<a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
</div>
</div>
<div id="license" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<a target="_blank" href="{{ meta.current_package.license.link }}">
<img src="{{ meta.current_package.license.image_link }}">
</a>
</div>
</div>
</div>
{% endif %}
</div>
<!-- FOOTER -->

8
templates/index/index.html
View File

@ -143,6 +143,14 @@
}
$(function () {
$('#index-form').on("keydown", function (e) {
if (e.key === "Enter") {
e.preventDefault();
goButtonClicked();
}
});
// Code that should be executed once DOM is ready goes here
$('#dropdown-predict').on('click', actionDropdownClicked);
$('#dropdown-search').on('click', actionDropdownClicked);

35
templates/modals/objects/delete_compound_modal.html
View File

@ -1,35 +0,0 @@
{% load static %}
<!-- Delete Compound -->
<div id="delete_compound_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Compound</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 Compound and associated Structures.
<form id="delete-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" id="hidden" name="hidden" value="delete-compound"/>
</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-compound-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function() {
$('#delete-compound-modal-submit').click(function(e){
e.preventDefault();
$('#delete-compound-modal-form').submit();
});
})
</script>

38
templates/modals/objects/delete_group_modal.html
View File

@ -1,38 +0,0 @@
{% load static %}
<!-- Delete Group -->
<div id="delete_group_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Group</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
<div class="alert alert-danger">
Clicking "Delete" will <strong>permanently</strong> delete the Group.
This action can't be undone!
</div>
<form id="delete-group-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" name="hidden" value="delete-group">
</form>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
<button type="button" class="btn btn-danger" id="delete-group-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function() {
$('#delete-group-modal-submit').click(function(e){
e.preventDefault();
$('#delete-group-modal-form').submit();
});
})
</script>

35
templates/modals/objects/delete_model_modal.html
View File

@ -1,35 +0,0 @@
{% 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>

35
templates/modals/objects/delete_node_modal.html
View File

@ -1,35 +0,0 @@
{% 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>

36
templates/modals/objects/delete_package_modal.html
View File

@ -1,36 +0,0 @@
{% load static %}
<!-- Delete Package -->
<div id="delete_package_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete Package</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
Deleting a Package deletes the very Package
as well as all Objects stored in the Package.
<form id="delete-package-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" id="hidden" name="hidden" value="delete-package"/>
</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-package-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function() {
$('#delete-package-modal-submit').click(function(e){
e.preventDefault();
$('#delete-package-modal-form').submit();
});
})
</script>

2
templates/modals/objects/delete_pathway_edge_modal.html
View File

@ -22,7 +22,7 @@
<option value="{{ e.url }}">{{ e.edge_label.name }}</option>
{% endfor %}
</select>
<input type="hidden" id="hidden" name="hidden" value="delete-edge"/>
<input type="hidden" id="hidden" name="hidden" value="delete"/>
</form>
<p></p>
<div id="delete_pathway_edge_image"></div>

35
templates/modals/objects/delete_pathway_modal.html
View File

@ -1,35 +0,0 @@
{% 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>

2
templates/modals/objects/delete_pathway_node_modal.html
View File

@ -22,7 +22,7 @@
<option value="{{ n.url }}">{{ n.default_node_label.name }}</option>
{% endfor %}
</select>
<input type="hidden" id="hidden" name="hidden" value="delete-node"/>
<input type="hidden" id="hidden" name="hidden" value="delete"/>
</form>
<p></p>
<div id="delete_pathway_node_image"></div>

35
templates/modals/objects/delete_reaction_modal.html
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@ -1,35 +0,0 @@
{% 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>

38
templates/modals/objects/delete_user_modal.html
View File

@ -1,38 +0,0 @@
{% load static %}
<!-- Delete User -->
<div id="delete_user_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete User</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
<div class="alert alert-danger">
Clicking "Delete" will <strong>permanently</strong> delete the User and associated data.
This action can't be undone!
</div>
<form id="delete-user-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" name="hidden" value="delete-user">
</form>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
<button type="button" class="btn btn-danger" id="delete-user-modal-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function() {
$('#delete-user-modal-submit').click(function(e){
e.preventDefault();
$('#delete-user-modal-form').submit();
});
})
</script>

1
templates/modals/objects/download_pathway_modal.html
View File

@ -29,6 +29,7 @@
$('#download-pathway-modal-submit').click(function (e) {
e.preventDefault();
$('#download-pathway-modal-form').submit();
$('#download_pathway_modal').modal('hide');
});
})

42
templates/modals/objects/generic_delete_modal.html Normal file
View File

@ -0,0 +1,42 @@
{% load static %}
<!-- Delete Object -->
<div id="generic_delete_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title">Delete {{ object_type|capfirst }}</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
{% if object_type == 'user' %}
Clicking "Delete" will <strong>permanently</strong> delete the User and associated data.
This action can't be undone!
{% else %}
Deletes the {{ object_type|capfirst }}. Related objects that depend on this {{ object_type|capfirst }}
will be deleted as well.
{% endif %}
<form id="generic-delete-modal-form" accept-charset="UTF-8" action="{{ current_object.url }}"
data-remote="true" method="post">
{% csrf_token %}
<input type="hidden" id="hidden" name="hidden" value="delete"/>
</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="generic-delete-modal-form-submit">Delete</button>
</div>
</div>
</div>
</div>
<script>
$(function () {
$('#generic-delete-modal-form-submit').click(function (e) {
e.preventDefault();
$('#generic-delete-modal-form').submit();
});
})
</script>

12
templates/modals/predict_modal.html
View File

@ -49,6 +49,18 @@
<iframe id="predict-modal-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
height="510"></iframe>
</div>
<label for="prediction-setting">Default Prediction Setting</label>
<select id="prediction-setting" name="prediction-setting" class="form-control"
data-width='100%'>
<option disabled>Select a Setting</option>
{% for s in meta.available_settings %}
<option value="{{ s.url }}"{% if s.id == meta.user.default_setting.id %}selected{% endif %}>
{{ s.name }}{% if s.id == meta.user.default_setting.id %} <i>(User default)</i>{% endif %}
</option>
{% endfor %}
</select>
</form>
</div>
<div class="modal-footer">

1
templates/objects/composite_rule.html
View File

@ -5,6 +5,7 @@
{% block action_modals %}
{% include "modals/objects/edit_rule_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="rule-detail">

2
templates/objects/compound.html
View File

@ -6,7 +6,7 @@
{% include "modals/objects/edit_compound_modal.html" %}
{% include "modals/objects/add_structure_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/delete_compound_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="compound-detail">

1
templates/objects/compound_structure.html
View File

@ -5,6 +5,7 @@
{% block action_modals %}
{% include "modals/objects/edit_compound_structure_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="compound-structure-detail">

6
templates/objects/edge.html
View File

@ -4,8 +4,8 @@
{% block action_modals %}
{# {% include "modals/objects/edit_edge_modal.html" %}#}
{# {% include "modals/objects/delete_edge_modal.html" %}#}
{% include "modals/objects/generic_set_scenario_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">
@ -20,7 +20,7 @@
style="padding-right:1em"></span></a>
<ul id="actionsList" class="dropdown-menu">
{% block actions %}
{# {% include "actions/objects/edge.html" %}#}
{% include "actions/objects/edge.html" %}
{% endblock %}
</ul>
</div>

2
templates/objects/group.html
View File

@ -5,7 +5,7 @@
{% block action_modals %}
{% include "modals/objects/edit_group_modal.html" %}
{% include "modals/objects/edit_group_member_modal.html" %}
{% include "modals/objects/delete_group_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="package-detail">

2
templates/objects/model.html
View File

@ -4,7 +4,7 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/delete_model_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<!-- Include required libs -->

2
templates/objects/node.html
View File

@ -5,7 +5,7 @@
{% block action_modals %}
{% include "modals/objects/edit_node_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/delete_node_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="node-detail">

20
templates/objects/package.html
View File

@ -6,7 +6,7 @@
{% include "modals/objects/edit_package_modal.html" %}
{% include "modals/objects/edit_package_permissions_modal.html" %}
{% include "modals/objects/set_license_modal.html" %}
{% include "modals/objects/delete_package_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="package-detail">
@ -52,23 +52,5 @@
</div>
{% if package.license %}
<p></p>
<div class="panel-group" id="license_accordion">
<div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
<div class="panel-title">
<a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
</div>
</div>
<div id="license" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<a target="_blank" href="{{ package.license.link }}">
<img src="{{ package.license.image_link }}">
</a>
</div>
</div>
</div>
{% endif %}
</div>
{% endblock content %}

2
templates/objects/pathway.html
View File

@ -86,7 +86,7 @@
{% 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/delete_pathway_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<p></p>

2
templates/objects/reaction.html
View File

@ -5,7 +5,7 @@
{% block action_modals %}
{% include "modals/objects/edit_reaction_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/delete_reaction_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="reaction-detail">

2
templates/objects/scenario.html
View File

@ -3,7 +3,7 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="scenario-detail">
<div class="panel panel-default">

1
templates/objects/simple_rule.html
View File

@ -5,6 +5,7 @@
{% block action_modals %}
{% include "modals/objects/edit_rule_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="rule-detail">

2
templates/objects/user.html
View File

@ -7,7 +7,7 @@
{% 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/delete_user_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="user-detail">

12
templates/search.html
View File

@ -79,6 +79,10 @@
allEmpty = true;
for (key in data) {
if (key === 'searchterm') {
continue;
}
if (data[key].length < 1) {
continue;
}
@ -176,8 +180,16 @@
$("#selPackages").selectpicker();
$("#search-button").on("click", search);
$("#searchbar").on("keydown", function (e) {
if (e.key === "Enter") {
e.preventDefault();
search(e);
}
});
});
{% if search_result %}
$('#searchbar').val('{{ search_result.searchterm }}')
handleSearchResponse("results", {{ search_result|safe }});
{% endif %}
</script>