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Remove software carpentries logo
[rnaseq-cwl-training.git]
/
bin
/
util.py
diff --git
a/bin/util.py
b/bin/util.py
index 522f5dfc6a00ff07cbcf64bb4c744745c47b02b5..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).
"""
# 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)
body = reader.read()
metadata_raw, metadata_yaml, body = split_metadata(path, body)
@@
-117,7
+117,7
@@
def read_markdown(parser, path):
# Parse Markdown.
cmd = 'ruby {0}'.format(parser)
p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE,
# 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)
stdout_data, stderr_data = p.communicate(body)
doc = json.loads(stdout_data)
@@
-144,7
+144,7
@@
def split_metadata(path, text):
metadata_raw = pieces[1]
text = pieces[2]
try:
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)
except yaml.YAMLError as e:
print('Unable to parse YAML header in {0}:\n{1}'.format(
path, e), file=sys.stderr)
@@
-160,8
+160,8
@@
def load_yaml(filename):
"""
try:
"""
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)
except (yaml.YAMLError, IOError) as e:
print('Unable to load YAML file {0}:\n{1}'.format(
filename, e), file=sys.stderr)