def fetch(self, data_spec):
"""Return the data described by the given specification.
:param dict data_spec: A data specification object
:returns: data
:raises ValidationError: when the validation check fails
>>> port = Port({'name': 'a', 'type': 'number', 'format': 'number'})
>>> port.fetch({'format': 'number', 'data': -1})
-1
"""
if self.auto_validate and not self.validate(data_spec):
raise ValidationError(self, data_spec)
if self.auto_convert:
_data = self.convert(data_spec, self.format)
data = _data.get('data')
elif self.format == data_spec.get('format'):
# TODO: This doesn't look right...
if 'data' in self and self['data'] is not None:
data = self['data']
else:
data = io.fetch(data_spec, task_input=self).get('data')
else:
raise Exception('Expected matching data formats ({} != {})' % (
str(data_spec['format']), str(self.format)
))
return data
def fetch(self, data_spec):
"""Return the data described by the given specification.
:param dict data_spec: A data specification object
:returns: data
:raises ValidationError: when the validation check fails
>>> port = Port({'name': 'a', 'type': 'number', 'format': 'number'})
>>> port.fetch({'format': 'number', 'data': -1})
-1
"""
if self.auto_validate and not self.validate(data_spec):
raise ValidationError(self, data_spec)
if self.auto_convert:
_data = self.convert(data_spec, self.format)
data = _data.get('data')
elif self.format == data_spec.get('format'):
# TODO: This doesn't look right...
if 'data' in self and self['data'] is not None:
data = self['data']
else:
data = io.fetch(data_spec, task_input=self).get('data')
else:
raise Exception('Expected matching data formats ({} != {})' %
(str(data_spec['format']), str(self.format)))
return data
def get_analysis(filename):
with open(filename) as f:
analysis = json.load(f)
if "script" not in analysis:
analysis["script"] = fetch(
{"mode": analysis.get("script_fetch_mode", "auto"), "url": analysis["script_uri"]}
)
return analysis
def convert(type, input, output, fetch=True, status=None, **kwargs):
"""
Convert data from one format to another.
:param type: The type specifier string of the input data.
:param input: A binding dict of the form
``{'format': format, 'data', data}``, where ``format`` is the format
specifier string, and ``data`` is the raw data to convert.
The dict may also be of the form
``{'format': format, 'uri', uri}``, where ``uri`` is the location of
the data (see :py:mod:`girder_worker.uri` for URI formats).
:param output: A binding of the form
``{'format': format}``, where ``format`` is the format
specifier string to convert the data to.
The binding may also be in the form
``{'format': format, 'uri', uri}``, where ``uri`` specifies
where to place the converted data.
:param fetch: Whether to do an initial data fetch before conversion
(default ``True``).
:returns: The output binding
dict with an additional field ``'data'`` containing the converted data.
If ``'uri'`` is present in the output binding, instead saves the data
to the specified URI and
returns the output binding unchanged.
"""
kwargs = kwargs.copy()
kwargs['auto_convert'] = False
if fetch:
input['data'] = io.fetch(input, **kwargs)
if input['format'] == output['format']:
data = input['data']
else:
data_descriptor = input
try:
conversion_path = converter_path(Validator(type, input['format']),
Validator(type, output['format']))
except NetworkXNoPath:
raise Exception('No conversion path from %s/%s to %s/%s' %
(type, input['format'], type, output['format']))
# Run data_descriptor through each conversion in the path
for conversion in conversion_path:
result = run(conversion, {'input': data_descriptor},
status=status,
**kwargs)
data_descriptor = result['output']
data = data_descriptor['data']
if status == utils.JobStatus.CONVERTING_OUTPUT:
job_mgr = kwargs.get('_job_manager')
set_job_status(job_mgr, utils.JobStatus.PUSHING_OUTPUT)
io.push(data, output, **kwargs)
return output
def get_analysis(filename):
with open(filename) as f:
analysis = json.load(f)
if 'script' not in analysis:
analysis['script'] = fetch({
'mode': analysis.get('script_fetch_mode', 'auto'),
'url': analysis['script_uri']
})
return analysis
def get_analysis(filename):
with open(filename) as f:
analysis = json.load(f)
if 'script' not in analysis:
analysis['script'] = fetch({
'mode':
analysis.get('script_fetch_mode', 'auto'),
'url':
analysis['script_uri']
})
return analysis
