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[rnaseq-cwl-training.git] / bin / util.py

diff --git a/bin/util.py b/bin/util.py
index a449f9fc55f2799e095fb7c5e7bcd43b4fec0292..0e16d869aaabdb44d468e85fa196582f3dc28988 100644 (file)
--- a/bin/util.py
+++ b/bin/util.py
@@ -1,4 +1,3 @@
-
 import sys
 import os
 import json
@@ -30,7 +29,7 @@ UNWANTED_FILES = [
 REPORTER_NOT_SET = []
 
 
-class Reporter(object):
+class Reporter:
     """Collect and report errors."""
 
     def __init__(self):
@@ -72,8 +71,9 @@ class Reporter(object):
             return location + ': ' + message
         elif isinstance(location, tuple):
             return '{0}:{1}: '.format(*location) + message
-        else:
-            assert False, 'Unknown item "{0}"'.format(item)
+
+        print('Unknown item "{0}"'.format(item), file=sys.stderr)
+        return NotImplemented
 
     @staticmethod
     def key(item):
@@ -84,8 +84,9 @@ class Reporter(object):
             return (location, -1, message)
         elif isinstance(location, tuple):
             return (location[0], location[1], message)
-        else:
-            assert False, 'Unknown item "{0}"'.format(item)
+
+        print('Unknown item "{0}"'.format(item), file=sys.stderr)
+        return NotImplemented
 
     def report(self, stream=sys.stdout):
         """Report all messages in order."""
@@ -104,7 +105,7 @@ def read_markdown(parser, path):
     """
 
     # Split and extract YAML (if present).
-    with open(path, 'r') as reader:
+    with open(path, 'r', encoding='utf-8') as reader:
         body = reader.read()
     metadata_raw, metadata_yaml, body = split_metadata(path, body)
 
@@ -116,7 +117,7 @@ def read_markdown(parser, path):
     # Parse Markdown.
     cmd = 'ruby {0}'.format(parser)
     p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE,
-              close_fds=True, universal_newlines=True)
+              close_fds=True, universal_newlines=True, encoding='utf-8')
     stdout_data, stderr_data = p.communicate(body)
     doc = json.loads(stdout_data)
 
@@ -143,7 +144,7 @@ def split_metadata(path, text):
         metadata_raw = pieces[1]
         text = pieces[2]
         try:
-            metadata_yaml = yaml.load(metadata_raw)
+            metadata_yaml = yaml.load(metadata_raw, Loader=yaml.SafeLoader)
         except yaml.YAMLError as e:
             print('Unable to parse YAML header in {0}:\n{1}'.format(
                 path, e), file=sys.stderr)
@@ -159,8 +160,8 @@ def load_yaml(filename):
     """
 
     try:
-        with open(filename, 'r') as reader:
-            return yaml.load(reader)
+        with open(filename, 'r', encoding='utf-8') as reader:
+            return yaml.load(reader, Loader=yaml.SafeLoader)
     except (yaml.YAMLError, IOError) as e:
         print('Unable to load YAML file {0}:\n{1}'.format(
             filename, e), file=sys.stderr)