Decode stdout/stderr before sending them to logger

In python 3, stdout/stderr are bytes objects, which get logged
incorrectly unless they get decoded into strings.

Author: xylar

mpas_analysis/shared/analysis_task.py

@@ -509,11 +509,11 @@ class AnalysisFormatter(logging.Formatter):  # {{{
 
     # printing error messages without a prefix because they are sometimes
     # errors and sometimes only warnings sent to stderr
-    err_fmt = "%(msg)s"
     dbg_fmt = "DEBUG: %(module)s: %(lineno)d: %(msg)s"
     info_fmt = "%(msg)s"
+    err_fmt = info_fmt
 
-    def __init__(self, fmt="%(levelno)s: %(msg)s"):
+    def __init__(self, fmt=info_fmt):
         logging.Formatter.__init__(self, fmt)
 
     def format(self, record):
@@ -561,7 +561,7 @@ def __init__(self, logger, log_level=logging.INFO):
 
     def write(self, buf):
         for line in buf.rstrip().splitlines():
-            self.logger.log(self.log_level, line.rstrip())
+            self.logger.log(self.log_level, str(line.rstrip()))
 
     def flush(self):
         pass

mpas_analysis/shared/climatology/mpas_climatology_task.py

@@ -429,8 +429,11 @@ def _compute_climatologies_with_ncclimo(self, inDirectory, outDirectory,
         stdout, stderr = process.communicate()
 
         if stdout:
-            self.logger.info(stdout)
+            stdout = stdout.decode('utf-8')
+            for line in stdout.split('\n'):
+                self.logger.info(line)
         if stderr:
+            stderr = stderr.decode('utf-8')
             for line in stderr.split('\n'):
                 self.logger.error(line)
 

mpas_analysis/shared/html/image_xml.py

@@ -164,6 +164,7 @@ def _provenance_command(root, history):  # {{{
     p = subprocess.Popen(['git', 'describe', '--always', '--dirty'],
                          stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     stdout, stderr = p.communicate()
+    stdout = stdout.decode('utf-8')
     if p.returncode == 0:
         githash = stdout.strip('\n')
     else:

mpas_analysis/shared/interpolation/remapper.py

@@ -319,8 +319,11 @@ def remap_file(self, inFileName, outFileName, variableList=None,
             stdout, stderr = process.communicate()
 
             if stdout:
-                logger.info(stdout)
+                stdout = stdout.decode('utf-8')
+                for line in stdout.split('\n'):
+                    logger.info(line)
             if stderr:
+                stderr = stderr.decode('utf-8')
                 for line in stderr.split('\n'):
                     logger.error(line)
 

mpas_analysis/shared/time_series/mpas_time_series_task.py

@@ -317,8 +317,11 @@ def _compute_time_series_with_ncrcat(self):
         stdout, stderr = process.communicate()
 
         if stdout:
-            self.logger.info(stdout)
+            stdout = stdout.decode('utf-8')
+            for line in stdout.split('\n'):
+                self.logger.info(line)
         if stderr:
+            stderr = stderr.decode('utf-8')
             for line in stderr.split('\n'):
                 self.logger.error(line)