import sys
+import os
import json
-import yaml
from subprocess import Popen, PIPE
+# Import this way to produce a more useful error message.
+try:
+ import yaml
+except ImportError:
+ print('Unable to import YAML module: please install PyYAML', file=sys.stderr)
+ sys.exit(1)
-class Reporter(object):
+
+# Things an image file's name can end with.
+IMAGE_FILE_SUFFIX = {
+ '.gif',
+ '.jpg',
+ '.png',
+ '.svg'
+}
+
+# Files that shouldn't be present.
+UNWANTED_FILES = [
+ '.nojekyll'
+]
+
+# Marker to show that an expected value hasn't been provided.
+# (Can't use 'None' because that might be a legitimate value.)
+REPORTER_NOT_SET = []
+
+
+class Reporter:
"""Collect and report errors."""
- def __init__(self, args):
+ def __init__(self):
"""Constructor."""
-
- super(Reporter, self).__init__()
self.messages = []
-
- def check_field(self, filename, name, values, key, expected):
+ def check_field(self, filename, name, values, key, expected=REPORTER_NOT_SET):
"""Check that a dictionary has an expected value."""
if key not in values:
self.add(filename, '{0} does not contain {1}', name, key)
+ elif expected is REPORTER_NOT_SET:
+ pass
+ elif type(expected) in (tuple, set, list):
+ if values[key] not in expected:
+ self.add(
+ filename, '{0} {1} value {2} is not in {3}', name, key, values[key], expected)
elif values[key] != expected:
- self.add(filename, '{0} {1} is {2} not {3}', name, key, values[key], expected)
-
+ self.add(filename, '{0} {1} is {2} not {3}',
+ name, key, values[key], expected)
def check(self, condition, location, fmt, *args):
"""Append error if condition not met."""
if not condition:
self.add(location, fmt, *args)
-
def add(self, location, fmt, *args):
"""Append error unilaterally."""
+ self.messages.append((location, fmt.format(*args)))
+
+ @staticmethod
+ def pretty(item):
+ location, message = item
if isinstance(location, type(None)):
- coords = ''
+ return message
elif isinstance(location, str):
- coords = '{0}: '.format(location)
+ return location + ': ' + message
elif isinstance(location, tuple):
- filename, line_number = location
- coords = '{0}:{1}: '.format(*location)
- else:
- assert False, 'Unknown location "{0}"/{1}'.format(location, type(location))
+ return '{0}:{1}: '.format(*location) + message
+
+ print('Unknown item "{0}"'.format(item), file=sys.stderr)
+ return NotImplemented
- self.messages.append(coords + fmt.format(*args))
+ @staticmethod
+ def key(item):
+ location, message = item
+ if isinstance(location, type(None)):
+ return ('', -1, message)
+ elif isinstance(location, str):
+ return (location, -1, message)
+ elif isinstance(location, tuple):
+ return (location[0], location[1], message)
+ print('Unknown item "{0}"'.format(item), file=sys.stderr)
+ return NotImplemented
def report(self, stream=sys.stdout):
- """Report all messages."""
+ """Report all messages in order."""
if not self.messages:
return
- for m in sorted(self.messages):
- print(m, file=stream)
+
+ for m in sorted(self.messages, key=self.key):
+ print(self.pretty(m), file=stream)
def read_markdown(parser, path):
"""
# Split and extract YAML (if present).
- metadata = None
- metadata_len = None
- with open(path, 'r') as reader:
+ with open(path, 'r', encoding='utf-8') as reader:
body = reader.read()
- pieces = body.split('---', 2)
- if len(pieces) == 3:
- try:
- metadata = yaml.load(pieces[1])
- except yaml.YAMLError as e:
- print('Unable to parse YAML header in {0}:\n{1}'.format(path, e))
- sys.exit(1)
- metadata_len = pieces[1].count('\n')
- body = pieces[2]
+ metadata_raw, metadata_yaml, body = split_metadata(path, body)
# Split into lines.
- offset = 0 if metadata_len is None else metadata_len
- lines = [(offset+i+1, l, len(l)) for (i, l) in enumerate(body.split('\n'))]
+ metadata_len = 0 if metadata_raw is None else metadata_raw.count('\n')
+ lines = [(metadata_len+i+1, line, len(line))
+ for (i, line) in enumerate(body.split('\n'))]
# Parse Markdown.
cmd = 'ruby {0}'.format(parser)
- p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, close_fds=True, universal_newlines=True)
+ p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE,
+ close_fds=True, universal_newlines=True, encoding='utf-8')
stdout_data, stderr_data = p.communicate(body)
doc = json.loads(stdout_data)
return {
- 'metadata': metadata,
+ 'metadata': metadata_yaml,
'metadata_len': metadata_len,
'text': body,
'lines': lines,
'doc': doc
}
+
+
+def split_metadata(path, text):
+ """
+ Get raw (text) metadata, metadata as YAML, and rest of body.
+ If no metadata, return (None, None, body).
+ """
+
+ metadata_raw = None
+ metadata_yaml = None
+
+ pieces = text.split('---', 2)
+ if len(pieces) == 3:
+ metadata_raw = pieces[1]
+ text = pieces[2]
+ try:
+ 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)
+ sys.exit(1)
+
+ return metadata_raw, metadata_yaml, text
+
+
+def load_yaml(filename):
+ """
+ Wrapper around YAML loading so that 'import yaml' is only needed
+ in one file.
+ """
+
+ try:
+ 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)
+ sys.exit(1)
+
+
+def check_unwanted_files(dir_path, reporter):
+ """
+ Check that unwanted files are not present.
+ """
+
+ for filename in UNWANTED_FILES:
+ path = os.path.join(dir_path, filename)
+ reporter.check(not os.path.exists(path),
+ path,
+ "Unwanted file found")
+
+
+def require(condition, message):
+ """Fail if condition not met."""
+
+ if not condition:
+ print(message, file=sys.stderr)
+ sys.exit(1)
projects / rnaseq-cwl-training.git / blobdiff