Cleanup (#52)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#52

epdb/models.py

@@ -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()

epdb/views.py

@@ -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}
+                    {"name": s.name, "url": s.full_url, "reviewed": True}
-                    for pw in reviewed_scenario_qs
+                    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()))
+        name = request.POST.get('name')
-        description = request.POST.get('description', s.DEFAULT_VALUES['description'])
+        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 = prediction_setting
-            pw.setting = pred_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:

templates/actions/objects/compound.html

@@ -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 %}

templates/actions/objects/compound_structure.html

@@ -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 %}

templates/actions/objects/edge.html

@@ -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 %}

templates/actions/objects/group.html

@@ -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">
             <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 %}

templates/actions/objects/model.html

@@ -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 %}

templates/actions/objects/node.html

@@ -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 %}

templates/actions/objects/package.html

@@ -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 %}

templates/actions/objects/pathway.html

@@ -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 %}

templates/actions/objects/reaction.html

@@ -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 %}

templates/actions/objects/rule.html

@@ -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 %}

templates/actions/objects/user.html

@@ -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 %}

templates/framework.html

@@ -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
+                        Predict Pathway
                     </a>
                 </li>
-                        <li>
+{#                <li class="dropdown">#}
-                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">
+{#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
-                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction
+{#                    <ul role="menu" class="dropdown-menu">#}
-                            </a>
+{#                        <li>#}
-                        </li>
+{#                            <a class="button" data-toggle="modal" data-target="#predict_modal">#}
-                    </ul>
+{#                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway#}
-                </li>
+{#                            </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 -->

templates/index/index.html

@@ -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);

templates/modals/objects/delete_compound_modal.html

@@ -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>

templates/modals/objects/delete_group_modal.html

@@ -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>

templates/modals/objects/delete_model_modal.html

@@ -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>

templates/modals/objects/delete_node_modal.html

@@ -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>

templates/modals/objects/delete_package_modal.html

@@ -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>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -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>

templates/modals/objects/delete_pathway_modal.html

@@ -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>

templates/modals/objects/delete_pathway_node_modal.html

@@ -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>

templates/modals/objects/delete_reaction_modal.html

@@ -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>

templates/modals/objects/delete_user_modal.html

@@ -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>

templates/modals/objects/download_pathway_modal.html

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

templates/modals/objects/generic_delete_modal.html

@@ -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>

templates/modals/predict_modal.html

@@ -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">

templates/objects/composite_rule.html

@@ -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">

templates/objects/compound.html

@@ -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">

templates/objects/compound_structure.html

@@ -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">

templates/objects/edge.html

@@ -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_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>

templates/objects/group.html

@@ -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">

templates/objects/model.html

@@ -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 -->

templates/objects/node.html

@@ -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">

templates/objects/package.html

@@ -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 %}

templates/objects/pathway.html

@@ -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>

templates/objects/reaction.html

@@ -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">

templates/objects/scenario.html

@@ -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">

templates/objects/simple_rule.html

@@ -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">

templates/objects/user.html

@@ -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">

templates/search.html

@@ -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>