class XnatSourceInputSpec(ArchiveSourceInputSpec):
project_id = traits.Str(mandatory=True, desc='The project ID')
server = traits.Str(mandatory=True, desc="The address of the XNAT server")
user = traits.Str(
mandatory=False,
desc=("The XNAT username to connect with in with if not "
"supplied it can be read from ~/.netrc (see "
"https://xnat.readthedocs.io/en/latest/static/tutorial.html"
"#connecting-to-a-server)"))
password = traits.Password(
mandatory=False,
desc=("The XNAT password corresponding to the supplied username, if "
"not supplied it can be read from ~/.netrc (see "
"https://xnat.readthedocs.io/en/latest/static/tutorial.html"
"#connecting-to-a-server)"))
cache_dir = Directory(
exists=True,
desc=("Path to the base directory where the downloaded"
"datasets will be cached"))
race_cond_delay = traits.Int(
usedefault=True,
default=30,
desc=("The amount of time to wait before checking that the required "
"dataset has been downloaded to cache by another process has "
"completed if they are attempting to download the same dataset"))
stagger = traits.Int(
mandatory=False,
desc=("Stagger the download of the required datasets by "
"stagger_delay * subject_id seconds to avoid sending too many "
"concurrent requests to XNAT"))
class XNATSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
_outputs = traits.Dict(traits.Str, value={}, usedefault=True)
server = traits.Str(mandatory=True,
requires=['user', 'pwd'],
xor=['config'])
user = traits.Str()
pwd = traits.Password()
config = File(mandatory=True, xor=['server'])
cache_dir = Directory(desc='')
project_id = traits.Str(desc='Project in which to store the outputs',
mandatory=True)
subject_id = traits.Str(desc='Set to subject id', mandatory=True)
experiment_id = traits.Str(desc='Set to workflow name', mandatory=True)
assessor_id = traits.Str(
desc=('Option to customize ouputs representation in XNAT - '
'assessor level will be used with specified id'),
mandatory=False,
xor=['reconstruction_id'])
reconstruction_id = traits.Str(
desc=('Option to customize ouputs representation in XNAT - '
'reconstruction level will be used with specified id'),
mandatory=False,
xor=['assessor_id'])
share = traits.Bool(
desc=('Option to share the subjects from the original project'
'instead of creating new ones when possible - the created '
'experiments are then shared backk to the original project'),
value=False,
usedefault=True,
mandatory=False,
)
def __setattr__(self, key, value):
if key not in self.copyable_trait_names():
self._outputs[key] = value
else:
super(XNATSinkInputSpec, self).__setattr__(key, value)
class XnatSinkInputSpecMixin(object):
project_id = traits.Str(mandatory=True, desc='The project ID')
server = traits.Str('https://mf-erc.its.monash.edu.au',
mandatory=True,
usedefault=True,
desc="The address of the MF server")
user = traits.Str(
mandatory=False,
desc=("The XNAT username to connect with in with if not "
"supplied it can be read from ~/.netrc (see "
"https://xnat.readthedocs.io/en/latest/static/tutorial.html"
"#connecting-to-a-server)"))
password = traits.Password(
mandatory=False,
desc=("The XNAT password corresponding to the supplied username, if "
"not supplied it can be read from ~/.netrc (see "
"https://xnat.readthedocs.io/en/latest/static/tutorial.html"
"#connecting-to-a-server)"))
cache_dir = Directory(
exists=True,
desc=("Path to the base directory where the downloaded"
"datasets will be cached"))
class XNATSourceInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
query_template = traits.Str(
mandatory=True,
desc=('Layout used to get files. Relative to base '
'directory if defined'))
query_template_args = traits.Dict(traits.Str,
traits.List(traits.List),
value=dict(outfiles=[]),
usedefault=True,
desc='Information to plug into template')
server = traits.Str(mandatory=True,
requires=['user', 'pwd'],
xor=['config'])
user = traits.Str()
pwd = traits.Password()
config = File(mandatory=True, xor=['server'])
cache_dir = Directory(desc='Cache directory')