nodes for querying biomine can now be selected using the rule browser.

workflows/segmine/library.py

@@ -21,8 +21,21 @@ def segmine_biomine_visualizer(input_dict):
 def segmine_rule_browser(input_dict):
     return {'node_list' : []}
 
-def segmine_rule_browser_finished(input_dict):
-    return {'node_list' : []}
+def segmine_rule_browser_finished(postdata, input_dict, output_dict):
+    rules = input_dict['rules']
+    widget_id = postdata.get('widget_id')[0]
+    selectedCell = postdata.get('selectedCell')[0]
+    key, _, idx = selectedCell.split('_')
+    node_list = []
+    rule = rules[int(idx)]
+    if key == 'terms':
+        terms = rule['description']['terms'] + \
+                rule['description']['interactingTerms']
+        node_list.extend([term['termID'] for term in terms])
+    elif key in ['coveredGenes', 'coveredTopGenes']:
+        genes = ['EntrezGene:%s' % gene for gene in rule[key]]
+        node_list.extend(genes)
+    return {'node_list' : node_list}
 
 def segmine_fc_gene_filter_finished(postdata, input_dict, output_dict):
     from orngBioinformatics import obiExpression as rankers

workflows/segmine/segs.py

@@ -6,6 +6,7 @@ import json
 
 def recursive_asdict(d):
     from suds.sudsobject import asdict
+    from suds.sax.text import Text
     """Convert Suds object into serializable format."""
     out = {}
     for k, v in asdict(d).iteritems():
@@ -17,8 +18,12 @@ def recursive_asdict(d):
                 if hasattr(item, '__keylist__'):
                     out[k].append(recursive_asdict(item))
                 else:
+                    if isinstance(item, Text):
+                        item = str(item)
                     out[k].append(item)
         else:
+            if isinstance(v, Text):
+                v = str(v)
             out[k] = v
     return out
 

workflows/segmine/templates/interactions/segmine_rule_browser.html

 <div id="widgetinteract-{{widget.pk}}" rel="{{widget.pk}}" class="widgetinteractdialog" title="{{widget.name}} wants your input!" width=800 height=600>
     <center>
-        <form>
+        <form id="segs_rules_form{{widget.pk}}">
             <table id="segs_rules{{widget.pk}}">
                 <thead>
                     <tr>
@@ -18,19 +18,19 @@
                     {% for rule in rules %}
                     <tr>
                         <td>{{ forloop.counter }}</td>
-                        <td>
+                        <td id="terms_{{widget.pk}}_{{forloop.counter0}}" class="selectable-cell">
                             {% for term in rule.description.terms %}
-                                <a data-toggle="tooltip" title="{{term.termID}}" id="{{term.termID}}">{{ term.name }}</a>{% if forloop.counter < rule.description.terms|length %},{% endif %}
+                                <span data-toggle="tooltip" title="{{term.termID}}" id="{{term.termID}}">{{ term.name }}</span>{% if forloop.counter < rule.description.terms|length %},{% endif %}
                             {% endfor %}
                             {% if rule.description.interactingTerms %}
                             <br/>INTERACTING:
                             {% endif %}
                             {% for term in rule.description.interactingTerms %}
-                                <a data-toggle="tooltip" title="{{term.termID}}" id="{{term.termID}}">{{ term.name }}</a>{% if forloop.counter < rule.description.interactingTerms|length %},{% endif %}
+                                <span data-toggle="tooltip" title="{{term.termID}}" id="{{term.termID}}">{{ term.name }}</span>{% if forloop.counter < rule.description.interactingTerms|length %},{% endif %}
                             {% endfor %}
                         </td>
-                        <td>{{rule.coveredTopGenes|length}}</td>
-                        <td>{{rule.coveredGenes|length}}</td>
+                        <td id="coveredTopGenes_{{widget.pk}}_{{forloop.counter0}}" class="selectable-cell">{{rule.coveredTopGenes|length}}</td>
+                        <td id="coveredGenes_{{widget.pk}}_{{forloop.counter0}}" class="selectable-cell">{{rule.coveredGenes|length}}</td>
                         <td>{{rule.fisher_pval|floatformat:3}}</td>
                         <td>{{rule.GSEA_pval|floatformat:3}}</td>
                         <td>{{rule.PAGE_pval|floatformat:3}}</td>
@@ -44,10 +44,15 @@
                     {% endfor %}
                 </tbody>
             </table>
+            <input type="hidden" id="selectedCell{{widget.pk}}" name="selectedCell" value=""/>
             <input type="hidden" name="widget_id" value="{{widget.pk}}"/>
         </form>
     </center>
     </div>
+    <style type="text/css">
+        .ui-selecting { background: #eee; }
+        .ui-selected { background: #dde; }
+    </style>
     <script type="text/javascript">
     $(function () {
         $(document).ready(function() {
@@ -57,9 +62,14 @@
                 "sPaginationType": "full_numbers"
             });
             $('#segs_rules{{widget.pk}}').selectable({
-              filter: "td"
+              filter: ".selectable-cell"
             });
         });
+        // Check which elements are selected on submit
+        $('.selectable-cell').click(function() {
+            var id = $(this).attr('id');
+            $('#selectedCell{{widget.pk}}').val(id);
+        });
     });
     </script>
 </div>
\ No newline at end of file