server: task.py store information about run status and run date

-file views display them

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

@@ -28,7 +28,8 @@ def help():
         response.headers['Access-Control-Max-Age'] = 86400
     return dict(message=T('help i\'m lost'))
 
-    
+
+## add a scheduller task to run vidjil on a specific sequence file
 def run_request():
     import gluon.contrib.simplejson
     if request.env.http_origin:
@@ -43,12 +44,6 @@ def run_request():
             error += "id sequence file needed, "
         if not "config_id" in request.vars:
             error += "id config needed, "
-            
-        row = db( ( db.data_file.config_id == request.vars["config_id" ] ) 
-                 & ( db.data_file.sequence_file_id == request.vars["sequence_file_id"] )  
-                 ).select()
-        if len(row) > 0 :
-            error += "run already done, "
         
         row2 = db( ( db.scheduler_task.args == '["'+request.vars["sequence_file_id"]+'", "'+request.vars["config_id"]+'"]' ) 
                  & ( db.scheduler_task.status != "FAILED"  )
@@ -61,7 +56,23 @@ def run_request():
             error += "run already registered, "
         
         if error == "" :
-            scheduler.queue_task('run', [request.vars["sequence_file_id"],request.vars["config_id"]]
+            
+            ## create or update data file state
+            row = db( ( db.data_file.config_id == request.vars["config_id" ] ) 
+             & ( db.data_file.sequence_file_id == request.vars["sequence_file_id"] )  
+             ).select()
+            
+            if len(row) > 0 : ## update
+                data_id = row[0].data_file.id
+                db.data_file[data_id] = dict(state = 'queued')
+            else:             ## create
+                data_id = db.data_file.insert(sequence_file_id = request.vars['sequence_file_id'],
+                                            config_id = request.vars['config_id'],
+                                            status = 'pending'
+                                            )
+            
+            ##add task to scheduller
+            scheduler.queue_task('run', [request.vars["sequence_file_id"],request.vars["config_id"], data_id]
                                  , repeats = 1, timeout = 6000)
             
             res = {"success": "true" , "msg": "request added" }

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

@@ -124,6 +124,8 @@ db.define_table('config',
 db.define_table('data_file',
                 Field('sequence_file_id', 'reference sequence_file'),
                 Field('config_id', 'reference config'),
+                Field('run_date','date'),
+                Field('status', 'string'),
                 Field('data_file', 'upload', length=1000000000000))
 
 

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

 # coding: utf8
 
-def run_vidjil(id_file, id_config):
+def run_vidjil(id_file, id_config, id_data):
+    import time, datetime
     from subprocess import Popen, PIPE, STDOUT, os
     
     ## les chemins d'acces a vidjil / aux fichiers de sequences
@@ -30,10 +31,12 @@ def run_vidjil(id_file, id_config):
     stream = open(data_filepath, 'rb')
     
     ## insertion dans la base de donnée
-    id = db.data_file.insert(sequence_file_id=id_file,
-                config_id=id_config,
-                data_file=stream
-                )
+    ts = time.time()
+    
+    db.data_file[id_data] = dict(status = 'ready',
+                                 run_date = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d'),
+                                 data_file = stream
+                                )
     
     db.commit()
     

server/web2py/applications/vidjil/views/patient/info.html

@@ -37,6 +37,7 @@
                 <td class="column2"> sampling date </td>
                 <td> info </td>
                 <td class="column4"> status </td>
+                <td class="column2"> vidjil run date </td>
                 <td class="column5"> </td>
                 <td class="column5"> </td>
                 <td class="column5"> </td>
@@ -62,9 +63,10 @@
                     <td> {{if row.data_file.id == None :}}
                         <span class="button" onclick="db.request('default/run_request', { 'sequence_file_id' : '{{=row.sequence_file.id}}' , 'config_id' : {{=config_id}} } )"> run >> </span>
                          {{else:}}
-                             ready
+                             {{=row.data_file.status}}
                          {{pass}}
                     </td>
+                    <td> {{=row.data_file.run_date}} </td>
                     <td> <a href="{{=URL('download', scheme='http', args=row.sequence_file.data_file)}}" >dl</a> </td>
                     <td onclick="db.call('file/edit', {'id' :'{{=row.sequence_file.id}}', 'patient_id' :'{{=request.vars['id']}}'} )" > e </td>
                     <td onclick="db.call('file/confirm', {'id' :'{{=row.sequence_file.id}}', 'patient_id' :'{{=request.vars['id']}}'} )" > X </td>