Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil

browser/js/com.js

@@ -82,7 +82,9 @@ function Com(flash_id, log_id, popup_id, data_id) {
 	    
         "database_timeout": "Cannot connect database, please retry in a few seconds",
     
-        "save_analysis": "change will be lost, are you sure you want to load another file ?"
+        "save_analysis": "You made some changes in the analysis of the previous patient"
+	    + "</br>that were not saved (patients → save analysis)."
+            + "</br>These changes will now be lost, do you want to proceed anyway?"
     }
     
     

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

@@ -12,9 +12,11 @@ if request.env.http_origin:
 def add(): 
     if not auth.has_permission('admin', 'patient', request.vars['id'], auth.user_id):
         res = {"success" : "false", "message" : "you need admin permission on this patient to add files"}
+        log.error(res)
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
     elif not auth.has_permission('upload', 'sequence_file', request.vars['id'], auth.user_id):
         res = {"success" : "false", "message" : "you don't have right to upload files"}
+        log.error(res)
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
     else:
         query = db((db.sequence_file.patient_id==request.vars['id'])).select()
@@ -46,6 +48,7 @@ def add_form():
         query = db((db.sequence_file.patient_id==request.vars['patient_id'])).select()
         for row in query :
             if row.filename == request.vars['filename'] :
+                log.error(res)
                 res = {"message": "this sequence file already exists for this patient"}
                 return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
             
@@ -69,6 +72,7 @@ def add_form():
         
     else :
         res = {"success" : "false", "message" : error}
+        log.error(res)
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
 
 
@@ -80,6 +84,7 @@ def edit():
     #    return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
     else:
         res = {"success" : "false", "message" : "you need admin permission to edit files"}
+        log.error(res)
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
         
 
@@ -126,6 +131,11 @@ def upload():
     if error=="" :
             
         mes = "file " + request.vars['id'] + " : "
+        res = {"message": mes + ": processing uploaded file",
+               "redirect": "patient/info",
+               "args" : {"id" : request.vars['id']}
+               }
+        log.info(res)
         if request.vars.file != None :
             f = request.vars.file
             db.sequence_file[request.vars["id"]] = dict(data_file = db.sequence_file.data_file.store(f.file, f.filename))
@@ -136,6 +146,7 @@ def upload():
         db.sequence_file[request.vars["id"]] = dict(size_file = size)
         
         res = {"message": mes}
+        log.info(res)
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
   
 
@@ -144,6 +155,7 @@ def confirm():
         return dict(message=T('confirm sequence file deletion'))
     else:
         res = {"success" : "false", "message" : "you need admin permission to delete this file"}
+        log.error(res)
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
         
 
@@ -163,6 +175,7 @@ def delete():
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
     else:
         res = {"success" : "false", "message" : "you need admin permission to delete this file"}
+        log.error(res)
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
     
 

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

@@ -249,9 +249,11 @@ class MsgUserAdapter(logging.LoggerAdapter):
             else:
                 msg = '?'
         ip = request.client
-        if ip in ips:
-            ip = "%s/%s" % (ip, ips[ip])
-        new_msg =  '%15s <%s> %s' % (ip, (auth.user.first_name if auth.user else ''), msg)
+        if ip:
+            for ip_prefix in ips:
+                if ip.startswith(ip_prefix):
+                    ip = "%s/%s" % (ip, ips[ip_prefix])
+        new_msg =  '%30s %12s %s' % (ip, ('<%s>' % auth.user.first_name if auth.user else ''), msg)
         return new_msg, kwargs
     
 #

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

@@ -3,7 +3,7 @@ import os
 import sys
 import defs
 
-TASK_TIMEOUT = 10 * 60
+TASK_TIMEOUT = 15 * 60
 
 def schedule_run(id_sequence, id_config):
     import time, datetime, sys, os.path
@@ -42,6 +42,7 @@ def schedule_run(id_sequence, id_config):
 
     if len(row3) > 0 :
         res = {"message": "run already registered"}
+        log.error(res)
         return res
 
 
@@ -56,7 +57,7 @@ def schedule_run(id_sequence, id_config):
     patient_name = db.patient[id_patient].first_name + " " + db.patient[id_patient].last_name
 
     res = {"redirect": "reload",
-           "message": "%s (%s) %s: process requested" % (patient_name, config_name, filename)}
+           "message": "[%s] (%s): process requested - %s - %s" % (data_id, config_name, patient_name, filename)}
 
     log.info(res)
     return res
@@ -133,6 +134,11 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, clean_before=False, clean_a
     ## l'output de Vidjil est stocké comme resultat pour l'ordonnanceur
     ## TODO parse result success/fail
 
+    config_name = db.config[id_config].name
+
+    res = {"message": "[%s] (%s): Vidjil finished - %s" % (id_data, config_name, out_folder)}
+    log.info(res)
+
     run_fuse(id_file, id_config, id_data, id_fuse, clean_before = False)
 
     return "SUCCESS"
@@ -190,6 +196,10 @@ def run_copy(id_file, id_config, id_data, id_fuse, clean_before=False, clean_aft
     ## l'output de Vidjil est stocké comme resultat pour l'ordonnanceur
     ## TODO parse result success/fail
 
+    config_name = db.config[id_config].name
+    res = {"message": "[%s] (%s): 'copy' finished - %s" % (id_data, config_name, filename)}
+    log.info(res)
+
     run_fuse(id_file, id_config, id_data, id_fuse, clean_before = False)
 
     return "SUCCESS"
@@ -260,6 +270,10 @@ def run_fuse(id_file, id_config, id_data, id_fuse, clean_before=True, clean_afte
         p = Popen(clean_cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
         p.wait()
     
+    config_name = db.config[id_config].name
+    res = {"message": "[%s] (%s): 'fuse' finished - %s" % (id_data, config_name, output_file)}
+    log.info(res)
+
     return "SUCCESS"