[Feature] Alias Support (#151)

Fixes #149

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#151

epdb/logic.py

@@ -691,6 +691,7 @@ class PackageManager(object):
                 struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4()
                 struc.name = structure["name"]
                 struc.description = structure["description"]
+                struc.aliases = structure.get("aliases", [])
                 struc.smiles = structure["smiles"]
                 struc.save()
 
@@ -728,6 +729,7 @@ class PackageManager(object):
             r.package = pack
             r.name = rule["name"]
             r.description = rule["description"]
+            r.aliases = rule.get("aliases", [])
             r.smirks = rule["smirks"]
             r.reactant_filter_smarts = rule.get("reactantFilterSmarts", None)
             r.product_filter_smarts = rule.get("productFilterSmarts", None)
@@ -747,6 +749,7 @@ class PackageManager(object):
             r.uuid = UUID(par_rule["id"].split("/")[-1]) if keep_ids else uuid4()
             r.name = par_rule["name"]
             r.description = par_rule["description"]
+            r.aliases = par_rule.get("aliases", [])
             r.save()
 
             mapping[par_rule["id"]] = r.uuid
@@ -766,6 +769,7 @@ class PackageManager(object):
             r.uuid = UUID(seq_rule["id"].split("/")[-1]) if keep_ids else uuid4()
             r.name = seq_rule["name"]
             r.description = seq_rule["description"]
+            r.aliases = seq_rule.get("aliases", [])
             r.save()
 
             mapping[seq_rule["id"]] = r.uuid
@@ -791,6 +795,7 @@ class PackageManager(object):
             r.uuid = UUID(reaction["id"].split("/")[-1]) if keep_ids else uuid4()
             r.name = reaction["name"]
             r.description = reaction["description"]
+            r.aliases = reaction.get("aliases", [])
             r.medlinereferences = (reaction["medlinereferences"],)
             r.multi_step = True if reaction["multistep"] == "true" else False
             r.save()
@@ -824,6 +829,7 @@ class PackageManager(object):
             pw.uuid = UUID(pathway["id"].split("/")[-1]) if keep_ids else uuid4()
             pw.name = pathway["name"]
             pw.description = pathway["description"]
+            pw.aliases = pathway.get("aliases", [])
             pw.save()
 
             mapping[pathway["id"]] = pw.uuid
@@ -836,6 +842,8 @@ class PackageManager(object):
                 n = Node()
                 n.uuid = UUID(node["id"].split("/")[-1]) if keep_ids else uuid4()
                 n.name = node["name"]
+                n.description = node.get("description")
+                n.aliases = node.get("aliases", [])
                 n.pathway = pw
                 n.depth = node["depth"]
                 n.default_node_label = CompoundStructure.objects.get(
@@ -862,6 +870,7 @@ class PackageManager(object):
                 e.name = edge["name"]
                 e.pathway = pw
                 e.description = edge["description"]
+                e.aliases = edge.get("aliases", [])
                 e.edge_label = Reaction.objects.get(uuid=mapping[edge["edgeLabel"]["id"]])
                 e.save()
 

epdb/views.py

@@ -300,6 +300,14 @@ def set_scenarios(current_user, attach_object, scenario_urls: List[str]):
     attach_object.set_scenarios(scens)
 
 
+def set_aliases(current_user, attach_object, aliases: List[str]):
+    if aliases == [""]:
+        aliases = []
+
+    attach_object.aliases = aliases
+    attach_object.save()
+
+
 def copy_object(current_user, target_package: "Package", source_object_url: str):
     # Ensures that source is readable
     source_package = PackageManager.get_package_by_url(current_user, source_object_url)
@@ -1160,10 +1168,19 @@ def package_compound(request, package_uuid, compound_uuid):
 
         if "selected-scenarios" in request.POST:
             selected_scenarios = request.POST.getlist("selected-scenarios")
-
             set_scenarios(current_user, current_compound, selected_scenarios)
             return redirect(current_compound.url)
 
+        if "aliases" in request.POST:
+            aliases = request.POST.getlist("aliases")
+
+            try:
+                set_aliases(current_user, current_compound, aliases)
+            except Exception as e:
+                return JsonResponse({"error": str(e)}, status=400)
+
+            return JsonResponse({"success": current_compound.url})
+
         new_compound_name = request.POST.get("compound-name", "").strip()
         new_compound_description = request.POST.get("compound-description", "").strip()
 
@@ -1311,6 +1328,16 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
             set_scenarios(current_user, current_structure, selected_scenarios)
             return redirect(current_structure.url)
 
+        if "aliases" in request.POST:
+            aliases = request.POST.getlist("aliases")
+
+            try:
+                set_aliases(current_user, current_structure, aliases)
+            except Exception as e:
+                return JsonResponse({"error": str(e)}, status=400)
+
+            return JsonResponse({"success": current_structure.url})
+
         selected_database = request.POST.get("selected-database", "").strip()
         external_identifier = request.POST.get("identifier", "").strip()
 
@@ -1472,6 +1499,16 @@ def package_rule(request, package_uuid, rule_uuid):
             set_scenarios(current_user, current_rule, selected_scenarios)
             return redirect(current_rule.url)
 
+        if "aliases" in request.POST:
+            aliases = request.POST.getlist("aliases")
+
+            try:
+                set_aliases(current_user, current_rule, aliases)
+            except Exception as e:
+                return JsonResponse({"error": str(e)}, status=400)
+
+            return JsonResponse({"success": current_rule.url})
+
         rule_name = request.POST.get("rule-name", "").strip()
         rule_description = request.POST.get("rule-description", "").strip()
 
@@ -1588,6 +1625,16 @@ def package_reaction(request, package_uuid, reaction_uuid):
             set_scenarios(current_user, current_reaction, selected_scenarios)
             return redirect(current_reaction.url)
 
+        if "aliases" in request.POST:
+            aliases = request.POST.getlist("aliases")
+
+            try:
+                set_aliases(current_user, current_reaction, aliases)
+            except Exception as e:
+                return JsonResponse({"error": str(e)}, status=400)
+
+            return JsonResponse({"success": current_reaction.url})
+
         new_reaction_name = request.POST.get("reaction-name", "").strip()
         new_reaction_description = request.POST.get("reaction-description", "").strip()
 
@@ -1807,6 +1854,16 @@ def package_pathway(request, package_uuid, pathway_uuid):
             set_scenarios(current_user, current_pathway, selected_scenarios)
             return redirect(current_pathway.url)
 
+        if "aliases" in request.POST:
+            aliases = request.POST.getlist("aliases")
+
+            try:
+                set_aliases(current_user, current_pathway, aliases)
+            except Exception as e:
+                return JsonResponse({"error": str(e)}, status=400)
+
+            return JsonResponse({"success": current_pathway.url})
+
         pathway_name = request.POST.get("pathway-name")
         pathway_description = request.POST.get("pathway-description")
 
@@ -1957,6 +2014,16 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
             set_scenarios(current_user, current_node, selected_scenarios)
             return redirect(current_node.url)
 
+        if "aliases" in request.POST:
+            aliases = request.POST.getlist("aliases")
+
+            try:
+                set_aliases(current_user, current_node, aliases)
+            except Exception as e:
+                return JsonResponse({"error": str(e)}, status=400)
+
+            return JsonResponse({"success": current_node.url})
+
         return HttpResponseBadRequest()
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
@@ -2073,6 +2140,16 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
             set_scenarios(current_user, current_edge, selected_scenarios)
             return redirect(current_edge.url)
 
+        if "aliases" in request.POST:
+            aliases = request.POST.getlist("aliases")
+
+            try:
+                set_aliases(current_user, current_edge, aliases)
+            except Exception as e:
+                return JsonResponse({"error": str(e)}, status=400)
+
+            return JsonResponse({"success": current_edge.url})
+
         return HttpResponseBadRequest()
 
     else:

templates/actions/objects/compound.html

@@ -3,6 +3,10 @@
         <a role="button" data-toggle="modal" data-target="#edit_compound_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Compound</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#add_structure_modal">
             <i class="glyphicon glyphicon-plus"></i> Add Structure</a>

templates/actions/objects/compound_structure.html

@@ -3,6 +3,10 @@
         <a role="button" data-toggle="modal" data-target="#edit_compound_structure_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>

templates/actions/objects/edge.html

@@ -1,4 +1,8 @@
 {% if meta.can_edit %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>

templates/actions/objects/node.html

@@ -3,6 +3,10 @@
         <a role="button" data-toggle="modal" data-target="#edit_node_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Node</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>

templates/actions/objects/pathway.html

@@ -31,6 +31,10 @@
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     {#    <li>#}
     {#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
     {#            <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}

templates/actions/objects/reaction.html

@@ -3,6 +3,10 @@
         <a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>

templates/actions/objects/rule.html

@@ -3,6 +3,10 @@
         <a role="button" data-toggle="modal" data-target="#edit_rule_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>

templates/modals/collections/import_legacy_package_modal.html

@@ -15,12 +15,12 @@
                       enctype="multipart/form-data">
                     {% csrf_token %}
                     <p>
-                        <label class="btn btn-primary" for="jsonFile">
+                        <label class="btn btn-primary" for="legacyJsonFile">
-                            <input id="jsonFile" name="file" type="file" style="display:none;"
+                            <input id="legacyJsonFile" name="file" type="file" style="display:none;"
-                                   onchange="$('#upload-file-info').html(this.files[0].name)">
+                                   onchange="$('#upload-legacy-file-info').html(this.files[0].name)">
                             Choose JSON File
                         </label>
-                        <span class="label label-info" id="upload-file-info"></span>
+                        <span class="label label-info" id="upload-legacy-file-info"></span>
                         <input type="hidden" value="import-legacy-package-json" name="hidden" readonly="">
                     </p>
                 </form>

templates/modals/objects/generic_set_aliases_modal.html

@@ -0,0 +1,169 @@
+{% load static %}
+
+<style>
+    .alias-container {
+        display: flex;
+        flex-wrap: wrap;
+        align-items: center;
+        border: 1px solid #ccc;
+        border-radius: 4px;
+        padding: 4px 6px;
+        cursor: text;
+        min-height: 38px;
+        background-color: #fff;
+    }
+
+    .alias {
+        display: inline-flex;
+        align-items: center;
+        background-color: #5bc0de;
+        color: white;
+        padding: 4px 8px;
+        margin: 3px 3px;
+        border-radius: 4px;
+        font-size: 13px;
+        line-height: 1.4;
+    }
+
+    .alias .remove {
+        margin-left: 6px;
+        cursor: pointer;
+        font-weight: bold;
+        line-height: 1;
+    }
+
+    .alias-input {
+        flex: 1;
+        min-width: 120px;
+        border: none;
+        outline: none;
+        margin: 3px 3px;
+        font-size: 14px;
+    }
+
+    .form-control.alias-container {
+        height: auto;
+        box-shadow: none;
+    }
+</style>
+
+<div class="modal fade bs-modal-lg" id="set_aliases_modal" tabindex="-1" aria-labelledby="set_aliases_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">×</span>
+                </button>
+                <h4 class="modal-title">Set Aliases for {{ current_object.name }}</h4>
+            </div>
+            <div class="modal-body">
+                <form id="set_aliases_modal_form" accept-charset="UTF-8" action="{{ current_object.url }}"
+                      data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="alias-input">Aliases:</label>
+                    <div class="form-control alias-container" id="alias-box">
+                        {% for alias in current_object.aliases %}
+                        <span class="alias">{{ alias|escape }}<span class="remove">&times;</span></span>
+                        {% endfor %}
+                        <input type="text" id="alias-input" class="alias-input" placeholder="Add Alias...">
+                    </div>
+                </form>
+                <div id="add-alias-error-message" class="alert alert-danger" role="alert" style="display: none">
+                </div>
+            </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="set_aliases_modal_form_submit">Submit</button>
+            </div>
+        </div>
+    </div>
+
+</div>
+<script>
+    $(function () {
+
+        function addAlias(aliasText) {
+            aliasText = aliasText.trim();
+            if (aliasText === '') return;
+
+            // Avoid duplicate aliass
+            var exists = false;
+            $('#alias-box .alias').each(function () {
+                if ($(this).text().replace('×', '').trim().toLowerCase() === aliasText.toLowerCase()) {
+                    exists = true;
+                    return false;
+                }
+            });
+
+            if (!exists) {
+                var aliasHtml = '<span class="alias">' + $('<div>').text(aliasText).html() +
+                    '<span class="remove">&times;</span></span>';
+                $(aliasHtml).insertBefore('#alias-input');
+            }
+
+            $('#alias-input').val('');
+        }
+
+        // Add alias when Enter is pressed
+        $('#alias-input').on('keypress', function (e) {
+            if (e.which === 13) {
+                e.preventDefault();
+                addAlias($(this).val());
+            }
+        });
+
+        // Add alias when input loses focus
+        $('#alias-input').on('blur', function () {
+            var val = $(this).val();
+            if (val.trim() !== '') {
+                addAlias(val);
+            }
+        });
+
+        // Remove alias when clicking ×
+        $('#alias-box').on('click', '.remove', function () {
+            $(this).closest('.alias').remove();
+        });
+
+        // Focus input when clicking the container
+        $('#alias-box').on('click', function () {
+            $('#alias-input').focus();
+        });
+
+
+        $('#set_aliases_modal_form_submit').on('click', function (e) {
+            e.preventDefault();
+
+            let aliases = [];
+            $('#alias-box .alias').each(function () {
+                aliases.push($(this).text().replace('×', '').trim())
+            });
+
+            if (aliases.length === 0) {
+                // Set empty string for deletion of all aliases
+                // If empty list is sent, its gets removed entirely from post data
+                aliases = ['']
+            }
+
+            formData = {
+                'aliases': aliases
+            }
+
+            $.ajax({
+                type: 'post',
+                data: formData,
+                url: '{{ current_object.url }}',
+                traditional: true,
+                success: function (data, textStatus) {
+                    window.location.href = data.success;
+                },
+                error: function (jqXHR, textStatus, errorThrown) {
+                    $('#add-alias-error-message').append('<p>Setting aliases failed!</p>');
+                    $('#add-alias-error-message').show();                }
+            });
+
+        });
+
+    });
+</script>

templates/modals/objects/generic_set_scenario_modal.html

@@ -64,8 +64,8 @@
 
             $('#set_scenario_modal_form_submit').on('click', function (e) {
                 e.preventDefault();
-                if ($('##scenario-select').val().length == 0) {
+                if ($('#scenario-select').val().length == 0) {
-                    $('##scenario-select').val([''])
+                    $('#scenario-select').val([''])
                 }
                 $('#set_scenario_modal_form').submit();
             });

templates/objects/composite_rule.html

@@ -2,12 +2,13 @@
 
 {% block content %}
 
-{% block action_modals %}
+    {% block action_modals %}
-{% include "modals/objects/edit_rule_modal.html" %}
+        {% include "modals/objects/edit_rule_modal.html" %}
-{% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
-{% include "modals/objects/generic_copy_object_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
-{% include "modals/objects/generic_delete_modal.html" %}
+        {% include "modals/objects/generic_copy_object_modal.html" %}
-{% endblock action_modals %}
+        {% include "modals/objects/generic_delete_modal.html" %}
+    {% endblock action_modals %}
 
 <div class="panel-group" id="rule-detail">
     <div class="panel panel-default">
@@ -32,6 +33,23 @@
             </p>
         </div>
 
+        {% if rule.aliases %}
+            <!-- Aliases -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="rule-aliases-link" data-toggle="collapse" data-parent="#rule-detail"
+                       href="#rule-aliases">Aliases</a>
+                </h4>
+            </div>
+            <div id="rule-aliases" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {% for alias in rule.aliases %}
+                        <a class="list-group-item">{{ alias }}</a>
+                    {% endfor %}
+                </div>
+            </div>
+        {% endif %}
+
         <!-- Reaction Patterns -->
         <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
             <h4 class="panel-title">

templates/objects/compound.html

@@ -4,6 +4,7 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_compound_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/add_structure_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_set_external_reference_modal.html" %}
@@ -37,6 +38,23 @@
                 </p>
             </div>
 
+            {% if compound.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="compound-aliases-link" data-toggle="collapse" data-parent="#compound-detail"
+                           href="#compound-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="compound-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in compound.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Description -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">

templates/objects/compound_structure.html

@@ -2,12 +2,13 @@
 
 {% block content %}
 
-{% block action_modals %}
+    {% block action_modals %}
-{% include "modals/objects/edit_compound_structure_modal.html" %}
+        {% include "modals/objects/edit_compound_structure_modal.html" %}
-{% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
-{% include "modals/objects/generic_set_external_reference_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
-{% include "modals/objects/generic_delete_modal.html" %}
+        {% include "modals/objects/generic_set_external_reference_modal.html" %}
-{% endblock action_modals %}
+        {% include "modals/objects/generic_delete_modal.html" %}
+    {% endblock action_modals %}
 
 <div class="panel-group" id="compound-structure-detail">
     <div class="panel panel-default">
@@ -33,34 +34,52 @@
         <!-- Image -->
         <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
             <h4 class="panel-title">
-                <a id="compound-image-link" data-toggle="collapse" data-parent="#compound-detail"
+                <a id="compound-structure-image-link" data-toggle="collapse" data-parent="#compound-structure-detail"
-                   href="#compound-image">Image Representation</a>
+                   href="#compound-structure-image">Image Representation</a>
             </h4>
         </div>
-        <div id="compound-image" class="panel-collapse collapse in">
+        <div id="compound-structure-image" class="panel-collapse collapse in">
             <div class="panel-body list-group-item">
                 <div id="image-div" align="center">
                     {{ compound_structure.as_svg|safe }}
                 </div>
             </div>
         </div>
+
         <!-- SMILES -->
         <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
             <h4 class="panel-title">
-                <a id="compound-smiles-link" data-toggle="collapse" data-parent="#compound-detail"
+                <a id="compound-structure-smiles-link" data-toggle="collapse" data-parent="#compound-structure-detail"
-                   href="#compound-smiles">SMILES Representation</a>
+                   href="#compound-structure-smiles">SMILES Representation</a>
             </h4>
         </div>
-        <div id="compound-smiles" class="panel-collapse collapse in">
+        <div id="compound-structure-smiles" class="panel-collapse collapse in">
             <div class="panel-body list-group-item">
                 {{ compound_structure.smiles }}
             </div>
         </div>
 
+        {% if compound_structure.aliases %}
+            <!-- Aliases -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="compound-structure-aliases-link" data-toggle="collapse" data-parent="#compound-structure-detail"
+                       href="#compound-structure-aliases">Aliases</a>
+                </h4>
+            </div>
+            <div id="compound-structure-aliases" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {% for alias in compound_structure.aliases %}
+                        <a class="list-group-item">{{ alias }}</a>
+                    {% endfor %}
+                </div>
+            </div>
+        {% endif %}
+
         {% if compound_structure.scenarios.all %}
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">
-                    <a id="compound_structure-scenario-link" data-toggle="collapse" data-parent="#compound-structure-detail"
+                    <a id="compound-structure-scenario-link" data-toggle="collapse" data-parent="#compound-structure-detail"
                        href="#compound-structure-scenario">Scenarios</a>
                 </h4>
             </div>

templates/objects/edge.html

@@ -4,6 +4,7 @@
 
     {% block action_modals %}
 {#        {% include "modals/objects/edit_edge_modal.html" %}#}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
@@ -39,6 +40,23 @@
                 </div>
             </div>
 
+            {% if edge.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="edge-aliases-link" data-toggle="collapse" data-parent="#edge-detail"
+                           href="#edge-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="edge-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in edge.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Image -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">

templates/objects/node.html

@@ -4,6 +4,7 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_node_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
@@ -42,6 +43,23 @@
                 </div>
             </div>
 
+            {% if node.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="node-aliases-link" data-toggle="collapse" data-parent="#node-detail"
+                           href="#node-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="node-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in node.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Image -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">

templates/objects/pathway.html

@@ -85,6 +85,7 @@
         {% include "modals/objects/download_pathway_image_modal.html" %}
         {% include "modals/objects/generic_copy_object_modal.html" %}
         {% include "modals/objects/edit_pathway_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/delete_pathway_node_modal.html" %}
         {% include "modals/objects/delete_pathway_edge_modal.html" %}
@@ -210,6 +211,23 @@
                 </div>
             </div>
 
+            {% if pathway.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="pathway-aliases-link" data-toggle="collapse" data-parent="#pathway-detail"
+                           href="#pathway-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="pathway-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in pathway.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             {% if pathway.scenarios.all %}
                 <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">

templates/objects/reaction.html

@@ -4,6 +4,7 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_reaction_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_copy_object_modal.html" %}
         {% include "modals/objects/generic_set_external_reference_modal.html" %}
@@ -41,6 +42,23 @@
                 </div>
             </div>
 
+            {% if reaction.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="reaction-aliases-link" data-toggle="collapse" data-parent="#reaction-detail"
+                           href="#reaction-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="reaction-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in reaction.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Image -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">

templates/objects/simple_rule.html

@@ -4,6 +4,7 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_rule_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_copy_object_modal.html" %}
         {% include "modals/objects/generic_delete_modal.html" %}
@@ -32,6 +33,23 @@
                 </p>
             </div>
 
+            {% if rule.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-aliases-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="rule-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in rule.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Representation -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">

tests/test_multigen_eval.py

@@ -74,6 +74,7 @@ class MultiGenTest(TestCase):
 
             shallow_pathway = graph_from_pathway(SPathway.from_pathway(pathway))
             pathway = graph_from_pathway(pathway)
+
             if not graphs_equal(shallow_pathway, pathway):
                 print("\n\nS", shallow_pathway.adj)
                 print("\n\nPW", pathway.adj)

tests/views/test_compound_views.py

@@ -340,3 +340,57 @@ class CompoundViewTest(TestCase):
         )
 
         self.assertEqual(self.user1_default_package.compounds.count(), 0)
+
+    def test_set_aliases(self):
+        alias_1 = "Alias 1"
+        alias_2 = "Alias 2"
+
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {"aliases": [alias_1, alias_2]},
+        )
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(len(c.aliases), 2)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {"aliases": [alias_1]},
+        )
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(len(c.aliases), 1)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "aliases": ""
+            },
+        )
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(len(c.aliases), 0)

tests/views/test_pathway_views.py

@@ -112,3 +112,57 @@ class PathwayViewTest(TestCase):
                 predicted_nodes.add(n.default_node_label.smiles)
 
         self.assertEqual(first_level_nodes, predicted_nodes)
+
+    def test_set_aliases(self):
+        alias_1 = "Alias 1"
+        alias_2 = "Alias 2"
+
+        response = self.client.post(
+            reverse("package pathway list", kwargs={"package_uuid": str(self.package.uuid)}),
+            {
+                "name": "Test Pathway",
+                "description": "Just a Description",
+                "predict": "predict",
+                "smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        pathway_url = response.url
+        pw = Pathway.objects.get(url=pathway_url)
+
+        response = self.client.post(
+            reverse(
+                "package pathway detail",
+                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
+            ),
+            {"aliases": [alias_1, alias_2]},
+        )
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(len(pw.aliases), 2)
+
+        response = self.client.post(
+            reverse(
+                "package pathway detail",
+                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
+            ),
+            {"aliases": [alias_1]},
+        )
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(len(pw.aliases), 1)
+
+        response = self.client.post(
+            reverse(
+                "package pathway detail",
+                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "aliases": ""
+            },
+        )
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(len(pw.aliases), 0)

tests/views/test_reaction_views.py

@@ -335,3 +335,56 @@ class ReactionViewTest(TestCase):
         )
 
         self.assertEqual(self.user1_default_package.reactions.count(), 0)
+
+    def test_set_aliases(self):
+        alias_1 = "Alias 1"
+        alias_2 = "Alias 2"
+
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        reaction_url = response.url
+        r = Reaction.objects.get(url=reaction_url)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {"aliases": [alias_1, alias_2]},
+        )
+
+        r = Reaction.objects.get(url=reaction_url)
+        self.assertEqual(len(r.aliases), 2)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {"aliases": [alias_1]},
+        )
+
+        r = Reaction.objects.get(url=reaction_url)
+        self.assertEqual(len(r.aliases), 1)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "aliases": ""
+            },
+        )
+
+        r = Reaction.objects.get(url=reaction_url)
+        self.assertEqual(len(r.aliases), 0)

tests/views/test_rule_views.py

@@ -258,3 +258,57 @@ class RuleViewTest(TestCase):
         )
 
         self.assertEqual(self.user1_default_package.rules.count(), 0)
+
+    def test_set_aliases(self):
+        alias_1 = "Alias 1"
+        alias_2 = "Alias 2"
+
+        response = self.client.post(
+            reverse("rules"),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {"aliases": [alias_1, alias_2]},
+        )
+
+        r = Rule.objects.get(url=rule_url)
+        self.assertEqual(len(r.aliases), 2)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {"aliases": [alias_1]},
+        )
+
+        r = Rule.objects.get(url=rule_url)
+        self.assertEqual(len(r.aliases), 1)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "aliases": ""
+            },
+        )
+
+        r = Rule.objects.get(url=rule_url)
+        self.assertEqual(len(r.aliases), 0)