updated Biomine search for plants

workflows/segmine/db/package_data.json

@@ -565,7 +565,7 @@
       "parameter_type": "text", 
       "variable": "maxnodes", 
       "parameter": true, 
-      "order": 1, 
+      "order": 2, 
       "description": "Search parameter maxnodes"
     }
   }, 
@@ -578,12 +578,12 @@
       "short_name": "dbs", 
       "uid": "cbdafcda-e0a8-4e8d-9684-f65023ec5b5b", 
       "default": "", 
-      "required": false, 
+      "required": true, 
       "multi": false, 
-      "parameter_type": "text", 
+      "parameter_type": null, 
       "variable": "dbname", 
-      "parameter": true, 
-      "order": 1, 
+      "parameter": false, 
+      "order": 3, 
       "description": "Name of the database to use"
     }
   }, 
@@ -3004,6 +3004,46 @@
       "description": "Rules as rows, their terms as columns."
     }
   }, 
+  {
+    "pk": 435, 
+    "model": "workflows.abstractwidget", 
+    "fields": {
+      "category": 44, 
+      "treeview_image": "", 
+      "windows_queue": false, 
+      "name": "Select Biomine database", 
+      "is_streaming": false, 
+      "uid": "91b39cdf-e6b2-4b4f-b5c9-38ecf2ba01bf", 
+      "interaction_view": "segmine_selectBMdatabase", 
+      "image": "", 
+      "package": "segmine", 
+      "static_image": "", 
+      "post_interact_action": "segmine_selectBMdatabase_finished", 
+      "user": null, 
+      "visualization_view": "", 
+      "streaming_visualization_view": "", 
+      "action": "segmine_selectBMdatabase", 
+      "wsdl_method": "", 
+      "wsdl": "", 
+      "interactive": true, 
+      "has_progress_bar": false, 
+      "order": 1, 
+      "description": "Calls the API of the new Biomine service to get the list of available databases."
+    }
+  }, 
+  {
+    "pk": 472, 
+    "model": "workflows.abstractoutput", 
+    "fields": {
+      "widget": 435, 
+      "name": "Database name", 
+      "short_name": "db", 
+      "variable": "database", 
+      "uid": "658dc964-06d2-4db9-8a82-f8d3947137ff", 
+      "order": 1, 
+      "description": "Name of the selected database"
+    }
+  }, 
   {
     "pk": 424, 
     "model": "workflows.abstractwidget", 

workflows/segmine/interaction_views.py

@@ -58,4 +58,22 @@ def segmine_hclustering(request, input_dict, output_dict, widget):
     djson = hclustering2json(hcluster)
     return render(request, 'interactions/segmine_hierarchical_clustering.html', {'widget': widget,
                                                                                  'dendrogram_json': djson,
-                                                                                 'nexamples': len(hcluster)})
+                                                                                 'nexamples': len(hcluster)})
\ No newline at end of file
+# end
+
+
+def segmine_selectBMdatabase(request, input_dict, output_dict, widget):
+    from urllib2 import urlopen
+    from json import loads
+
+    listdb_url = 'http://biomine.ijs.si/list_databases'
+    try:
+        result = loads(urlopen(listdb_url).read())
+        dbs = [str(x) for x in result['databases']]
+    except:
+        raise IOError('Error while calling Biomine API.')
+
+    return render(request, 'interactions/segmine_selectBMdatabase.html', {'widget': widget,
+                                                                          'databases': dbs})
+# end
+

workflows/segmine/library.py

@@ -902,4 +902,15 @@ def segmine_biomine_search_plants(input_dict):
     if 'error' in result:
         raise Exception(result['error'])
 
-    return {'bmgraph': result['graph']}
+    return {'bmgraph': result['graph']}
\ No newline at end of file
+# end
+
+
+def segmine_selectBMdatabase(input_dict):
+    return {'database': None}
+
+
+def segmine_selectBMdatabase_finished(postdata, input_dict, output_dict):
+    dbid = str(postdata['selected_database'][0])
+    return {'database': dbid}
+# end

workflows/segmine/templates/interactions/segmine_selectBMdatabase.html

+<div id="widgetinteract-{{ widget.pk }}"
+     rel="{{ widget.pk }}"
+     class="widgetinteractdialog"
+     title="{{ widget.name }} wants your input!"
+     width=320 height=160>
+
+    <form id="interactionform-{{ widget.pk }}" name="interactionform-{{ widget.pk }}">
+        <label><strong>Available databases:</strong></label>
+        <select id="dbselect">
+            {% for dbid in databases %}
+                {% if forloop.counter0 == 0 %}
+                    <option value="{{ dbid }}" selected>{{ dbid }}</option>
+                {% else %}
+                    <option value="{{ dbid }}">{{ dbid }}</option>
+                {% endif %}
+            {% endfor %}
+        </select>
+        <input type="hidden" name="widget_id" value="{{ widget.pk }}">
+        {% for dbid in databases %}
+            {% if forloop.counter0 == 0 %}
+                <input type="hidden" id="dbInput" name="selected_database" value="{{ dbid }}">
+            {% endif %}
+        {% empty %}
+            <input type="hidden" id="dbInput" name="selected_database" value="">
+        {% endfor %}
+
+    </form>
+</div>
+
+
+<style type="text/css">
+</style>
+
+<script>
+    $("#dbselect").change(function () {
+        $("#dbInput").val($("#dbselect").val());
+    });
+</script>
+
+
+

workflows/segmine/visualization_views.py

@@ -7,6 +7,7 @@ from django.shortcuts import render
 import os
 import json
 
+
 def segmine_biomine_visualizer(request, input_dict, output_dict, widget):
     from mothra.settings import MEDIA_ROOT
     from workflows.helpers import ensure_dir
@@ -19,8 +20,9 @@ def segmine_biomine_visualizer(request, input_dict, output_dict, widget):
     return render(request, 'visualizations/segmine_biomine_visualizer.html', 
                   {'widget':widget, 'filename' : filename})
 
+
 def segmine_rank_plotter(request, input_dict, output_dict, widget):
     scores = input_dict['ranks']
     scores = zip(*scores)[1]
     return render(request, 'visualizations/segmine_rank_plotter.html', 
-                  {'widget':widget, 'gene_ranks' : json.dumps(scores)})
+                  {'widget': widget, 'gene_ranks': json.dumps(scores)})
\ No newline at end of file