Improve logging

studyprocessor.py

@@ -40,7 +40,7 @@ class StudyProcessor(Aggregator, HDF5Container):
 
 
         # log id
-        self.log_id = "study {}".format(tag)
+        self.log_id = "study({})".format(tag)
 
 
 
@@ -156,7 +156,7 @@ class StudyProcessor(Aggregator, HDF5Container):
                 prop[run] = getter(run, num)
             else:
                 prop[run] = getter(run)
-        return np.array(list(prop.keys()))
+        return np.array(list(prop.values()))
 
     def time_avg(self, name, start=None, end=None, span=None, unit_time=U.Myr, group="/series", select=None):
         """Do the time average and quantiles of a time series
@@ -295,6 +295,7 @@ class StudyProcessor(Aggregator, HDF5Container):
     def _extract_sinks_from_log(self, series, log_filename, run):
         cmd_grep = f"grep 'Number of sink' {log_filename} -A 2"
         content = os.popen(cmd_grep).readlines()
+        block_err = [] # Block that will ill parsed
         for i in range(0, len(content), 4):
             try:
                 nb_sink = np.int(content[i].split("=")[1])
@@ -309,11 +310,11 @@ class StudyProcessor(Aggregator, HDF5Container):
                 series["time"][run].append(time)
 
             except (ValueError, IndexError):
-                self._log(
-                    "Error encountered in parsing {} (grepped block {})".format(
-                        log_filename, i
-                    ),
-                    "WARNING",
+                block_err.append(i)
+        
+        if len(block_err) > 0:
+            self.logger.warning(
+                    f"Errors encountered in parsing {log_filename} (grepped blocks {block_err})"
                 )
         return series
 
@@ -323,6 +324,7 @@ class StudyProcessor(Aggregator, HDF5Container):
         nb_stellar = list(map(lambda s: int(s.split()[1]), content))
         line_numbers = list(map(lambda s: int(s.split(":")[0]), content))
         current_line = 0
+        block_err = [] # Block that will ill parsed
         logfile = open(log_filename)
         for i in range(0, len(line_numbers)):
             try:
@@ -346,11 +348,11 @@ class StudyProcessor(Aggregator, HDF5Container):
                     stellar_objects["id"][run].append(id)
 
             except (ValueError, IndexError):
-                self._log(
-                    "[stellar] Error encountered in parsing {} (grepped block {})".format(
-                        log_filename, i
-                    ),
-                    "WARNING",
+                block_err.append(i)
+        
+        if len(block_err) > 0:
+            self.logger.warning(
+                    f"Errors encountered in parsing {log_filename} (grepped blocks {block_err})"
                 )
         logfile.close()
         return stellar_objects
@@ -368,6 +370,7 @@ class StudyProcessor(Aggregator, HDF5Container):
     def _extract_fine_step_from_log(self, series, log_filename, run):
         cmd_grep = "grep 'Fine step' {} ".format(log_filename)
         content = os.popen(cmd_grep).readlines()
+        block_err = [] # Block that will ill parsed
         for i in range(0, len(content)):
             try:
                 data = content[i].replace("=", " ").split()
@@ -384,11 +387,11 @@ class StudyProcessor(Aggregator, HDF5Container):
                 series["mem_cells"][run].append(mempc1)
                 series["mem_parts"][run].append(mempc2)
             except (ValueError, IndexError):
-                self._log(
-                    "[fine step] Error encountered in parsing {} (grepped block {})".format(
-                        log_filename, i
-                    ),
-                    "WARNING",
+                block_err.append(i)
+        
+        if len(block_err) > 0:
+            self.logger.warning(
+                    f"Error encountered in parsing {log_filename} (grepped blocks {block_err})"
                 )
         return series