models/task.py, controllers/{file,patient}.py: streamline log messages

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

@@ -140,12 +140,14 @@ def add_form():
         
         #add a default sample_set for this sequence file
         id_sample_set = db.sample_set.insert(sample_type="sequence_file")
+        ids_sample_set = []
         
         id_sample_set_membership = db.sample_set_membership.insert(sample_set_id=id_sample_set,
                                                                   sequence_file_id=id)
         #add sequence_file to a run sample_set
         if run_id is not None :
             run_sample_set_id = db.run[run_id].sample_set_id
+            ids_sample_set += [run_sample_set_id] # for logging
             id_sample_set_membership_run = db.sample_set_membership.insert(sample_set_id=run_sample_set_id,
                                                                   sequence_file_id=id)
             redirect_args = {"id" : run_sample_set_id}
@@ -153,13 +155,14 @@ def add_form():
         #add sequence_file to a patient sample_set
         if patient_id is not None :
             patient_sample_set_id = db.patient[patient_id].sample_set_id
+            ids_sample_set += [patient_sample_set_id] # for logging
             id_sample_set_membership_patient = db.sample_set_membership.insert(sample_set_id=patient_sample_set_id,
                                                                   sequence_file_id=id)
             redirect_args = {"id" : patient_sample_set_id}
         
         
         res = {"file_id" : id,
-               "message": "file %s : upload started: %s" % (id, request.vars['filename']),
+               "message": "(%s) file {%s} : upload started: %s" % (','.join(map(str,ids_sample_set)), id, request.vars['filename']),
                "redirect": "sample_set/index",
                "args" : redirect_args
                }
@@ -270,7 +273,7 @@ def edit_form():
             error += "date (wrong format), "
             
     if error=="" :
-        mes = "file " + str(request.vars['id']) + " : "
+        mes = "file {%s}: " % request.vars['id']
         filename = db.sequence_file[request.vars['id']].filename
         if request.vars['filename'] != "":
             filename = request.vars['filename']
@@ -305,7 +308,7 @@ def edit_form():
         
         
         res = {"file_id" : request.vars["id"],
-               "message": "file %s: metadata saved" % request.vars["id"],
+               "message": "file {%s}: metadata saved" % request.vars["id"],
                "redirect": "sample_set/index",
                "args" : redirect_args
                }
@@ -325,11 +328,7 @@ def upload():
         error += "no sequence file with this id"
 
     if not error:
-        patient_id = db((db.sequence_file.id == request.vars["id"])
-                        &(db.sample_set_membership.sequence_file_id == db.sequence_file.id)
-                        &(db.patient.sample_set_id == db.sample_set_membership.sample_set_id)
-                        ).select(db.patient.id).first()
-        mes += " file %s (patient %s) " % (db.sequence_file[request.vars['id']].filename, patient_id['id'])
+        mes += " file {%s} " % (request.vars['id'])
         res = {"message": mes + "processing uploaded file",
                "redirect": "patient/info",
                "args" : {"id" : request.vars['id']}

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

@@ -326,7 +326,7 @@ def add_form():
 
             res = {"redirect": "sample_set/index",
                    "args" : { "id" : id_sample_set },
-                   "message": patient_name + ": patient added"}
+                   "message": "(%s) patient %s added" % (id_sample_set, patient_name) }
             log.info(res)
 
             if (id % 100) == 0:

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

@@ -627,7 +627,7 @@ def schedule_pre_process(sequence_file_id, pre_process_id):
     db.sequence_file[sequence_file_id] = dict(pre_process_scheduler_task_id = task.id)
     
     res = {"redirect": "reload",
-           "message": "[%s] (%s): process requested" % (sequence_file_id, pre_process_id)}
+           "message": "{%s} (%s): process requested" % (sequence_file_id, pre_process_id)}
 
     log.info(res)
     return res
@@ -701,7 +701,7 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
         stream = open(filepath, 'rb')
     except IOError:
         print "!!! Pre-process failed, no result file"
-        res = {"message": "[%s] p%s: 'pre_process' FAILED - %s" % (sequence_file_id, pre_process_id, output_file)}
+        res = {"message": "{%s} p%s: 'pre_process' FAILED - %s" % (sequence_file_id, pre_process_id, output_file)}
         log.error(res)
         db.sequence_file[sequence_file_id] = dict(pre_process_flag = "FAILED")
         db.commit()
@@ -726,7 +726,7 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
         p = Popen(clean_cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
         p.wait()
     
-    res = {"message": "[%s] p%s: 'pre_process' finished - %s" % (sequence_file_id, pre_process_id, output_file)}
+    res = {"message": "{%s} p%s: 'pre_process' finished - %s" % (sequence_file_id, pre_process_id, output_file)}
     log.info(res)
 
     return "SUCCESS"