make it possible to run compute_extra on its own

See #3452

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

@@ -158,7 +158,14 @@ def run_contamination():
     log.error(res)
     return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
 
-
+def run_extra():
+    task = scheduler.queue_task('compute_extra', pvars=dict(id_file=request.vars["sequence_file_id"],
+                                                            id_config=request.vars["config_id"],
+                                                            min_threshold=5))
+    res = {"success" : "true",
+           "processId" : task.id}
+    log.debug(res)
+    return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
 
 def checkProcess():
     task = db.scheduler_task[request.vars["processId"]]

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

@@ -722,7 +722,8 @@ def getStatData(results_file_ids):
         (db.sequence_file.id == db.results_file.sequence_file_id) &
         (db.config.id == db.results_file.config_id)
         ).select(
-            db.results_file.data_file.with_alias("results_file"), db.results_file.id.with_alias("results_file_id"),
+            db.results_file.sequence_file_id, db.results_file.config_id,
+            db.results_file.data_file.with_alias("data_file"), db.results_file.id.with_alias("results_file_id"),
             db.sequence_file.data_file.with_alias("sequence_file"),
             db.sample_set.id.with_alias("set_id"),
             db.sample_set.sample_type.with_alias("sample_type"),
@@ -767,12 +768,14 @@ def getStatData(results_file_ids):
         d = {}
         set_type = res['sample_type']
         headers = getStatHeaders()
-        d = getFusedStats(res['results_file'], res, d)
+        d = getFusedStats(res['data_file'], res, d)
         for head, htype, model in headers:
             if htype == 'db':
                 d[head] = res[head]
             d[head] = model.decorate(d[head])
             log.debug("%s: %s" % (head, d[head]))
+        d['sequence_file_id'] = res['results_file']['sequence_file_id']
+        d['config_id'] = res['results_file']['config_id']
         data.append(d)
     return data
 

server/web2py/applications/vidjil/models/task.py

@@ -91,14 +91,15 @@ def compute_contamination(sequence_file_id, results_file_id, config_id):
 
     return result
     
-def compute_num_clones(id_file, id_config, id_data, min_threshold, clean_before=True, clean_after=False):
-    out_folder = defs.DIR_OUT_VIDJIL_ID % id_data
-    output_filename = defs.BASENAME_OUT_VIDJIL_ID % id_data
-    out_extra = out_folder+'/'+output_filename+'.vidjil.extra'
+def compute_extra(id_file, id_config, min_threshold):
     result = {}
     results_file = db((db.results_file.sequence_file_id == id_file) &
                       (db.results_file.config_id == id_config)
                     ).select().first()
+    id_data = results_file.id
+    out_folder = defs.DIR_OUT_VIDJIL_ID % id_data
+    output_filename = defs.BASENAME_OUT_VIDJIL_ID % id_data
+    out_extra = out_folder+'/'+output_filename+'.vidjil.extra'
     with open(defs.DIR_RESULTS+results_file.data_file, "rb") as rf:
         try:
             d = json.load(rf)
@@ -175,6 +176,10 @@ def schedule_fuse(sample_set_ids, config_ids):
         task = scheduler.queue_task('refuse', [args],
                                     repeats = 1, timeout = defs.TASK_TIMEOUT)
 
+def schedule_compute_extra(id_file, id_config, min_threshold):
+    args = [id_file, id_config,  min_threshold]
+    task = scheduler.queue_task('compute_extra', args, repeats=1, timeout=defs.TASK_TIMEOUT)
+
 def run_vidjil(id_file, id_config, id_data, grep_reads,
                clean_before=False, clean_after=False):
     from subprocess import Popen, PIPE, STDOUT, os
@@ -914,7 +919,7 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
 from gluon.scheduler import Scheduler
 scheduler = Scheduler(db, dict(vidjil=run_vidjil,
                                compute_contamination=compute_contamination,
-                               compute_num_clones=compute_num_clones,
+                               compute_extra=compute_extra,
                                mixcr=run_mixcr,
                                igrec=run_igrec,
                                none=run_copy,

server/web2py/applications/vidjil/views/sample_set/multi_sample_stats.html

@@ -10,6 +10,7 @@
                 <span class="content {{=h}}">{{=h}}</span>
             </td>
             {{ pass }}
+            <td></td>
         </tr>
         </thead>
         <tbody>
@@ -20,6 +21,9 @@
                         <span class="content {{=h}}">{{=res[h]}}</span>
                     </td>
                     {{ pass }}
+                    <td>
+                       <span class="pointer" onclick="db.call('default/run_extra', { 'sequence_file_id' : '{{=res["sequence_file_id"]}}', 'config_id' : {{=res["config_id"]}} } )"><i class="icon-cog-2" title="Run the selected configuration for this file"></i></span>
+                    </td>
                 </tr>
             {{ pass }}
         </tbody>