controllers/clonedb.py: Controller to call the CloneDB

Actually it is not a good idea that the client directly calls
the CloneDB. Indeed some tags from the CloneDB directly refers
to data on the server-side. Therefore the server can bring valuable
informations.

That's what we do know: the client calls a controller which calls
the CloneDB. The controller then adds other information useful to the client
(URL of the sample sets, name of the sample sets).

server/web2py/applications/vidjil/controllers/clonedb.py

+# coding: utf8
+import gluon.contrib.simplejson, datetime
+import vidjil_utils
+import time
+import os
+import sys
+import imp
+
+if request.env.http_origin:
+    response.headers['Access-Control-Allow-Origin'] = request.env.http_origin  
+    response.headers['Access-Control-Allow-Credentials'] = 'true'
+    response.headers['Access-Control-Max-Age'] = 86400
+
+
+def index():
+    '''
+    The request should receive two parameters:
+    - sequences: a list of comma-separated DNA sequences to be searched in the CloneDB
+    - sample_set_id: the sample set we're coming from
+    '''
+    if not auth.user:
+        return response.json({'error': 'Access denied'})
+
+    if request.vars['sequences'] == None or request.vars['sequences'] == ''\
+       or request.vars['sample_set_id'] == None:
+        return response.json({'error': 'Malformed request'})
+
+    return search_clonedb(request.vars['sequences'].split(','), int(request.vars['sample_set_id']))
+
+def search_clonedb(sequences, sample_set_id):
+    sys.path.insert(1, os.path.abspath(defs.DIR_CLONEDB))
+    import grep_clones
+    clonedb = imp.load_source('clonedb', defs.DIR_CLONEDB+os.path.sep+'clonedb.cgi')
+
+    results = []
+    for sequence in sequences:
+        options = clonedb.build_grep_clones_options({'sequence': sequence+' -sample_set:%d' % sample_set_id})
+        args = grep_clones.parser.parse_args(options)
+        log.debug(args)
+        occurrences = grep_clones.launch_search(args)
+        for occ in occurrences:
+            if 'tags' in occ and 'sample_set' in occ['tags']:
+                info = get_info_of_viewable_sample_set([int(sample_id) for sample_id in occ['tags']['sample_set']], int(occ['tags']['config_id'][0]))
+                occ['tags']['sample_set_viewable'] = info['viewable']
+                occ['tags']['sample_set_name'] = info['name']
+                config_db = db.config[occ['tags']['config_id'][0]]
+                occ['tags']['config_name'] = [config_db.name if config_db else None]
+        results.append(occurrences)
+    return response.json(results)
+
+def get_info_of_viewable_sample_set(sample_sets, config):
+    info = {'viewable': [], 'name': []}
+    for sample_id in sample_sets:
+        viewable = auth.can_view_sample_set(sample_id, auth.user)
+        info['viewable'].append(viewable)
+        if viewable:
+            info['name'].append(get_sample_name(sample_id))
+        else:
+            info['name'].append(None)
+    return info