Remove software carpentries logo

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

diff --git a/bin/util.py b/bin/util.py
index 084d5f46cbf8d8997de8b18b67de970a15db61ce..0e16d869aaabdb44d468e85fa196582f3dc28988 100644 (file)
--- a/bin/util.py
+++ b/bin/util.py
@@ -105,7 +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)
 
@@ -117,8 +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)
-    body = str(body.encode('utf-8'))
+              close_fds=True, universal_newlines=True, encoding='utf-8')
     stdout_data, stderr_data = p.communicate(body)
     doc = json.loads(stdout_data)
 
@@ -145,7 +144,7 @@ def split_metadata(path, text):
         metadata_raw = pieces[1]
         text = pieces[2]
         try:
-            metadata_yaml = yaml.load(metadata_raw, Loader=yaml.FullLoader)
+            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)
@@ -161,8 +160,8 @@ def load_yaml(filename):
     """
 
     try:
-        with open(filename, 'r') as reader:
-            return yaml.load(reader, Loader=yaml.FullLoader)
+        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)