def _expand_stages(cls):
ocs = {c.__name__: c for c in subclasses(object)}
for type_ in (cls._submission, cls._curation):
for name in type_:
cname, *rest = name.split('.', 1)
c = ocs[cname]
suffix = ''
if rest:
suffix = '.' + ''.join(rest)
for sc in subclasses(c):
type_.append(sc.__name__ + suffix)
def getOnts():
return tuple(
l for l in subclasses(ParcOnt) if l.__name__ != 'parcBridge'
and not hasattr(l, f'_{l.__name__}__pythonOnly') and (
l.__module__ != 'nifstd_tools.parcellation'
if __name__ == '__main__' or __name__ == '__init__' else
l.__module__ != '__main__' and l.__module__ != '__init__'))
def _triples(self):
from nifstd_tools.parcellation import Artifact
yield from Artifact.class_triples()
# OH LOOK PYTHON IS BEING AN AWFUL LANGUAGE AGAIN
for art_type in subclasses(
Artifact
): # this is ok because all subclasses are in this file...
# do not comment this out it is what makes the
# upper classes in the artifacts hierarchy
yield from art_type.class_triples()
for artifact in self._artifacts:
yield from artifact
class parcBridge(ParcOnt):
""" Main bridge for importing the various files that
make up the parcellation ontology. """
# setup
path = 'ttl/bridge/'
filename = 'parcellation-bridge'
name = 'Parcellation Bridge'
imports = (
(
g[subclass.__name__]
if subclass.__name__ in g and subclass.__module__ ==
'nifstd_tools.parcellation' # parcellation is insurance for name reuse
else subclass) for g in (globals(), ) for subclass in subclasses(
LabelsBase
) # XXX wow, well apparently __main__.Class != module.Class
if not hasattr(subclass, f'_{subclass.__name__}__pythonOnly'))
@property
def __imports(self):
for subclass in subclasses(LabelsBase):
if not hasattr(subclass, f'_{subclass.__name__}__pythonOnly'):
yield subclass()
def __imports(self):
for subclass in subclasses(LabelsBase):
if not hasattr(subclass, f'_{subclass.__name__}__pythonOnly'):
yield subclass()
def _artifacts(self):
for collector in subclasses(Collector):
if collector.__module__ != 'nifstd_tools.parcellation': # just run __main__
yield from collector.arts()
top_tag = 'METADATA' # LOL OH WOW >_< this just keeps getting better
mimetype = 'application/x.vnd.zeiss.czi.ZISRAWSUBBLOCK.METADATA+xml' # TODO
def _extract(self):
# TODO has time information and stage and focus
# seems to be using file naming conventions to match
# sidecar to tiff (urg)
return {}
class ExtractMSXMLExcel(XmlSource):
""" MS-XML for Excel.
https://en.wikipedia.org/wiki/Microsoft_Office_XML_formats
"""
top_tag = '{urn:schemas-microsoft-com:office:spreadsheet}Workbook'
# not clear that this is really xml metadata, it might count as data
mimetype = 'application/vnd.ms-excel+xml' # this isn't real, but close enough
def _extract(self):
return {}
ExtractXml.classes = (*[c for c in subclasses(XmlSource)], XmlSource)
# FIXME not entirely clear that I am using type correctly here
[register_type(None, cls.mimetype) for cls in ExtractXml.classes
# NotXml has no mimetype
if cls.mimetype is not None]
