Download Pathway Functionality (#38)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#38

epdb/models.py

@@ -920,6 +920,46 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
 
         return json.dumps(res)
 
+    def to_csv(self) -> str:
+        import csv
+        import io
+
+        rows = []
+        rows.append([
+            'SMILES',
+            'name',
+            'depth',
+            'probability',
+            'rule_names',
+            'rule_ids',
+            'parent_smiles',
+        ])
+        for n in self.nodes.order_by('depth'):
+            cs = n.default_node_label
+            row = [cs.smiles, cs.name, n.depth]
+
+            edges = self.edges.filter(end_nodes__in=[n])
+            if len(edges):
+                for e in edges:
+                    _row = row.copy()
+                    _row.append(e.kv.get('probability'))
+                    _row.append(','.join([r.name for r in e.edge_label.rules.all()]))
+                    _row.append(','.join([r.url for r in e.edge_label.rules.all()]))
+                    _row.append(e.start_nodes.all()[0].default_node_label.smiles)
+                    rows.append(_row)
+            else:
+                row += [None, None, None, None]
+                rows.append(row)
+
+        buffer = io.StringIO()
+
+        writer = csv.writer(buffer)
+        writer.writerows(rows)
+
+        buffer.seek(0)
+
+        return buffer.getvalue()
+
     @staticmethod
     @transaction.atomic
     def create(package: 'Package', smiles: str, name: Optional[str] = None, description: Optional[str] = None):

epdb/views.py

@@ -1254,6 +1254,14 @@ def package_pathway(request, package_uuid, pathway_uuid):
         if request.GET.get("last_modified", False):
             return JsonResponse({'modified': current_pathway.modified.strftime('%Y-%m-%d %H:%M:%S')})
 
+        if request.GET.get("download", False) == "true":
+            filename = f"{current_pathway.name.replace(' ', '_')}_{current_pathway.uuid}.csv"
+            csv_pw = current_pathway.to_csv()
+            response = HttpResponse(csv_pw, content_type='text/csv')
+            response['Content-Disposition'] = f'attachment; filename="{filename}"'
+
+            return response
+
         context = get_base_context(request)
         context['title'] = f'enviPath - {current_package.name} - {current_pathway.name}'
 

templates/actions/objects/pathway.html

@@ -9,19 +9,24 @@
     </li>
     <li role="separator" class="divider"></li>
     <li>
-        <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
+        <a class="button" data-toggle="modal" data-target="#download_pathway_modal">
-            <i class="glyphicon glyphicon-plus"></i> Edit Pathway</a>
+            <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway</a>
     </li>
-{#    <li>#}
+    <li role="separator" class="divider"></li>
-{#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
+    <li>
-{#            <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}
+        <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
-{#    </li>#}
+            <i class="glyphicon glyphicon-edit"></i> Edit Pathway</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>#}
+    {#    </li>#}
     <li role="separator" class="divider"></li>
     <li>
         <a class="button" data-toggle="modal" data-target="#delete_pathway_node_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
     </li>
-        <li>
+    <li>
         <a class="button" data-toggle="modal" data-target="#delete_pathway_edge_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
     </li>

templates/modals/objects/download_pathway_modal.html

@@ -0,0 +1,35 @@
+{% load static %}
+<!-- Download Pathway -->
+<div id="download_pathway_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Download 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">
+                By clicking on Download the Pathway will be converted into a CSV and directly downloaded.
+                <form id="download-pathway-modal-form" accept-charset="UTF-8" action="{{ pathway.url }}"
+                      data-remote="true" method="GET">
+                    <input type="hidden" name="download" value="true"/>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="download-pathway-modal-submit">Download</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+
+        $('#download-pathway-modal-submit').click(function (e) {
+            e.preventDefault();
+            $('#download-pathway-modal-form').submit();
+        });
+
+    })
+</script>

templates/objects/pathway.html

@@ -50,6 +50,7 @@
     {% block action_modals %}
         {% include "modals/objects/add_pathway_node_modal.html" %}
         {% include "modals/objects/add_pathway_edge_modal.html" %}
+        {% include "modals/objects/download_pathway_modal.html" %}
         {% include "modals/objects/edit_pathway_modal.html" %}
         {% include "modals/objects/delete_pathway_node_modal.html" %}
         {% include "modals/objects/delete_pathway_edge_modal.html" %}