file.py file forms, add all invovled groups to group_ids for tags

Samples had not been updated to include multiple groups, this commit not
only served to fix this, but also takes the opportunity to include all
the involved groups when auto-completing samples

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

@@ -57,17 +57,18 @@ def add():
         patient_id = None
         run_id = None
         generic_id = None
-        group_id = None
+        group_ids = []
         if sample_set.sample_type == defs.SET_TYPE_GENERIC:
             generic_id = db( db.generic.sample_set_id == request.vars["id"]).select()[0].id
-            group_id = get_set_group(sample_set.sample_type, generic_id)
+            group_ids.append(get_set_group(sample_set.sample_type, generic_id))
         if sample_set.sample_type == defs.SET_TYPE_PATIENT:
             patient_id = db( db.patient.sample_set_id == request.vars["id"]).select()[0].id
-            group_id = get_set_group(sample_set.sample_type, patient_id)
+            group_ids.append(get_set_group(sample_set.sample_type, patient_id))
         if sample_set.sample_type == defs.SET_TYPE_RUN:
             run_id = db( db.run.sample_set_id == request.vars["id"]).select()[0].id
-            group_id = get_set_group(sample_set.sample_type, run_id)
-        
+            group_ids.append(get_set_group(sample_set.sample_type, run_id))
+
+        group_ids = [int(gid) for gid in group_ids]
 		
 	query_pre_process = db(
             db.pre_process>0
@@ -103,7 +104,7 @@ def add():
                    sample_type = sample_set.sample_type,
                    run = run,
                    source_module_active = source_module_active,
-                   group_id = group_id)
+                   group_ids = group_ids)
 
 def manage_filename(filename):
     filepath = ""
@@ -282,11 +283,12 @@ def edit():
         patient_list, patient = get_sample_set_list(defs.SET_TYPE_PATIENT, relevant_ids['patient'])
         run_list, run = get_sample_set_list(defs.SET_TYPE_RUN, relevant_ids['run'])
 
-        group_id = None
+        group_ids = []
         for key in relevant_ids:
             if (relevant_ids[key] is not None):
-                group_id = get_set_group(key, relevant_ids[key])
-                break
+                group_ids.append(get_set_group(key, relevant_ids[key]))
+
+        group_ids = [int(gid) for gid in group_ids]
 
         source_module_active = hasattr(defs, 'FILE_SOURCE') and hasattr(defs, 'FILE_TYPES')
         return dict(message = T('edit file'),
@@ -300,7 +302,7 @@ def edit():
                    file = db.sequence_file[request.vars["id"]],
                    sample_type = request.vars['sample_type'],
                    source_module_active = source_module_active,
-                   group_id = group_id)
+                   group_ids = group_ids)
 
     else:
         return error_message("you need admin permission to edit files")

server/web2py/applications/vidjil/views/file/add.html

@@ -90,7 +90,7 @@
             </tr>
             <tr>
                 <td><label for="file_info" id="file_info__label">info: </label></td>
-                <td><textarea onfocus="new VidjilAutoComplete().setupAtWho(this);" data-needs-atwho="true" data-group-id="{{=group_id}}" class="text" id="file_info" name="file_info" cols="60" rows="8"></textarea></td>
+                <td><textarea onfocus="new VidjilAutoComplete().setupAtWho(this);" data-needs-atwho="true" data-group-ids="{{=group_ids}}" class="text" id="file_info" name="file_info" cols="60" rows="8"></textarea></td>
                 <td></td>
             </tr>
             <tr>

server/web2py/applications/vidjil/views/file/edit.html

@@ -98,7 +98,7 @@ info = db.sequence_file[request.vars["id"]]
             </tr>
             <tr>
                 <td><label for="file_info" id="file_info__label">info: </label></td>
-                <td><textarea onfocus="new VidjilAutoComplete().setupAtWho(this);" data-needs-atwho="true" data-group-id="{{=group_id}}" class="text" id="file_info" name="file_info" cols="60" rows="12">{{=file.info}}</textarea></td>
+                <td><textarea onfocus="new VidjilAutoComplete().setupAtWho(this);" data-needs-atwho="true" data-group-ids="{{=group_ids}}" class="text" id="file_info" name="file_info" cols="60" rows="12">{{=file.info}}</textarea></td>
                 <td></td>
             </tr>
             <tr>