added new Biomine search for plants (new JSI hosted Biomine instance) and some small fixes

workflows/segmine/db/package_data.json

@@ -506,6 +506,100 @@
       "description": "Best path"
     }
   }, 
+  {
+    "pk": 427, 
+    "model": "workflows.abstractwidget", 
+    "fields": {
+      "category": 44, 
+      "treeview_image": "", 
+      "windows_queue": false, 
+      "name": "Biomine search (plants)", 
+      "is_streaming": false, 
+      "uid": "f4955e19-df67-4092-9bf3-8a76987755bd", 
+      "interaction_view": "", 
+      "image": "", 
+      "package": "segmine", 
+      "static_image": "", 
+      "post_interact_action": "", 
+      "user": null, 
+      "visualization_view": "", 
+      "streaming_visualization_view": "", 
+      "action": "segmine_biomine_search_plants", 
+      "wsdl_method": "", 
+      "wsdl": "", 
+      "interactive": false, 
+      "has_progress_bar": false, 
+      "order": 1, 
+      "description": "Calls the Biomine search engine (for plant data, updated version at JSI)."
+    }
+  }, 
+  {
+    "pk": 1068, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 427, 
+      "name": "Query nodes", 
+      "short_name": "que", 
+      "uid": "54934b0c-9ef7-456d-bfa6-37dab60a863a", 
+      "default": "", 
+      "required": true, 
+      "multi": false, 
+      "parameter_type": null, 
+      "variable": "qterms", 
+      "parameter": false, 
+      "order": 1, 
+      "description": "A list of query nodes"
+    }
+  }, 
+  {
+    "pk": 1069, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 427, 
+      "name": "Max nodes", 
+      "short_name": "mxn", 
+      "uid": "0fe196ff-1e7b-4047-917a-2d828f52f3ae", 
+      "default": "", 
+      "required": false, 
+      "multi": false, 
+      "parameter_type": "text", 
+      "variable": "maxnodes", 
+      "parameter": true, 
+      "order": 1, 
+      "description": "Search parameter maxnodes"
+    }
+  }, 
+  {
+    "pk": 1070, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 427, 
+      "name": "Database", 
+      "short_name": "dbs", 
+      "uid": "cbdafcda-e0a8-4e8d-9684-f65023ec5b5b", 
+      "default": "", 
+      "required": false, 
+      "multi": false, 
+      "parameter_type": "text", 
+      "variable": "dbname", 
+      "parameter": true, 
+      "order": 1, 
+      "description": "Name of the database to use"
+    }
+  }, 
+  {
+    "pk": 460, 
+    "model": "workflows.abstractoutput", 
+    "fields": {
+      "widget": 427, 
+      "name": "Biomine graph", 
+      "short_name": "bmg", 
+      "variable": "bmgraph", 
+      "uid": "7f87c504-dcad-469b-84b7-67f3b1de2322", 
+      "order": 1, 
+      "description": "A graph in .bmg format"
+    }
+  }, 
   {
     "pk": 193, 
     "model": "workflows.abstractwidget", 

workflows/segmine/library.py

@@ -879,3 +879,27 @@ def segmine_ruletable2attribute_union_intersection(input_dict):
         intersection = [constants.ENTREZ_GENE_PREFIX + ':' + x for x in intersection]
 
     return {'atrUnion': union, 'atrInter': intersection}
+
+
+def segmine_biomine_search_plants(input_dict):
+    import urllib
+    import urllib2
+    import json
+    url = 'http://biomine.ijs.si/api'
+
+    qterms = input_dict['qterms']
+    maxnodes = input_dict['maxnodes'].strip()
+    dbname = input_dict['dbname'].strip()
+
+    qdict = {'query': ' '.join(qterms)}
+    if maxnodes:
+        qdict['maxnodes'] = int(maxnodes)
+    if dbname:
+        qdict['database'] = str(dbname)
+
+    params = urllib.urlencode(qdict)
+    result = json.loads(urllib2.urlopen(url, params).read())
+    if 'error' in result:
+        raise Exception(result['error'])
+
+    return {'bmgraph': result['graph']}
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workflows/segmine/templates/visualizations/segmine_biomine_visualizer.html

-<div id="widgetvisualization-{{widget.pk}}" rel="{{widget.pk}}" class="widgetvisualizationdialog" title="{{widget.name}} visualization" width=700 height=600>
+<div id="widgetvisualization-{{widget.pk}}" rel="{{widget.pk}}"
+     class="widgetvisualizationdialog" title="{{widget.name}} visualization" width="900" height="700" >
     <applet code="biomine/bmvis/BMVis.class"
             archive="{{STATIC_URL}}segmine/bmvis.jar"
-            width=650 height=500>
+            width=850 height=590>
             <param name="graph" value="{{ MEDIA_URL }}{{ filename }}"> 
     </applet>
 </div>
\ No newline at end of file