def __init__(self, dirname):
"""
Represents a single metadata.yaml file.
Parameters
----------
fn : filename of YAML- or JSON-formatted config file
"""
self.dirname = dirname
self._build_metadata()
fn = os.path.join(self.dirname, 'metadata.yaml')
if not os.path.exists(fn):
raise ValueError("Can't find {0}".format(fn))
self.metadata = yaml.load(open(fn))
schema = yaml.load(utils.get_resource('metadata_schema.yaml'))
jsonschema.validate(self.metadata, schema)
self.study = self.metadata['study']
self.label = self.metadata['study']['label']
self.study.setdefault('short_label', self.label)
self.study.setdefault('long_label', self.study['short_label'])
self.study['PMID'] = str(self.study.get('PMID', ''))
self.tracks = [Data(d, self.dirname) for d in self.metadata['tracks']]
# If description is blank or missing, fill in the contents of the
# README.
if not self.study.get('description', ''):
readme = self._find_readme()
if readme:
self.study['description'] = open(readme).read()
def __init__(self, dirname):
"""
Represents a single metadata.yaml file.
Parameters
----------
fn : filename of YAML- or JSON-formatted config file
"""
self.dirname = dirname
self._build_metadata()
fn = os.path.join(self.dirname, 'metadata.yaml')
if not os.path.exists(fn):
raise ValueError("Can't find {0}".format(fn))
self.metadata = yaml.load(open(fn))
schema = yaml.load(utils.get_resource('metadata_schema.yaml'))
jsonschema.validate(self.metadata, schema)
self.study = self.metadata['study']
self.label = self.metadata['study']['label']
self.study.setdefault('short_label', self.label)
self.study.setdefault('long_label', self.study['short_label'])
self.study.setdefault('description', self.study['long_label'])
self.tracks = [Data(d, self.dirname) for d in self.metadata['tracks']]
def __init__(self, dirname):
"""
Represents a single metadata.yaml file.
Parameters
----------
fn : filename of YAML- or JSON-formatted config file
"""
self.dirname = dirname
self._build_metadata()
fn = os.path.join(self.dirname, 'metadata.yaml')
if not os.path.exists(fn):
raise ValueError("Can't find {0}".format(fn))
self.metadata = yaml.load(open(fn))
schema = yaml.load(utils.get_resource('metadata_schema.yaml'))
jsonschema.validate(self.metadata, schema)
self.study = self.metadata['study']
self.label = self.metadata['study']['label']
self.study.setdefault('short_label', self.label)
self.study.setdefault('long_label', self.study['short_label'])
self.study.setdefault('description', self.study['long_label'])
self.tracks = [Data(d, self.dirname) for d in self.metadata['tracks']]
def __init__(self, fn):
self.group = yaml.load(open(fn))
self.filename = fn
self.dirname = os.path.dirname(fn)
self.group.setdefault('short_label', self.group['name'])
self.group.setdefault('long_label', self.group['name'])
schema = yaml.load(utils.get_resource('group_schema.yaml'))
jsonschema.validate(self.group, schema)
self.studies = [
Study(os.path.join(self.dirname, s)) for s in self.group['studies']
]
def __init__(self, fn):
self.group = yaml.load(open(fn))
self.filename = fn
self.dirname = os.path.dirname(fn)
self.group.setdefault('short_label', self.group['name'])
self.group.setdefault('long_label', self.group['name'])
schema = yaml.load(utils.get_resource('group_schema.yaml'))
jsonschema.validate(self.group, schema)
self.studies = [
Study(os.path.join(self.dirname, s))
for s in self.group['studies']
]
