def graph(self):
if not hasattr(self, '_graph'):
self._graph = populateFromJsonLd(OntGraph(), self.asJsonLd())
OntCuries.populate(self._graph)
self.populateHeader(self._graph)
return self._graph
def graph(self):
g = OntGraph()
OntCuries.populate(g)
self.populate(g)
g.bind('local', self.context)
g.bind('apinatomy', readable) # FIXME populate from store
g.bind('elements', elements)
return g
def graphFromGithub(link, verbose=False):
# mmmm no validation
# also caching probably
if verbose:
log.info(link)
g = OntGraph().parse(f'{link}?raw=true', format='turtle')
OntCuries.populate(g)
return g
def populate(self, graph=None):
""" Populate a graph, or if no graph is provided
populate a new empty graph from the current
content. (Also useful for debug) """
if graph is None:
graph = OntGraph()
[graph.add(t) for t in self.triples]
OntCuries.populate(graph)
return graph
def import_tree(graph, ontologies, **kwargs):
for ontology in ontologies:
thisfile = Path(ontology).name
print(thisfile)
OntCuries.populate(graph)
j = graph.asOboGraph('owl:imports', restriction=False)
try:
t, te = creatTree(*Query(f'NIFTTL:{thisfile}', 'owl:imports', 'OUTGOING', 30), json=j, prefixes=dict(graph.namespace_manager), **kwargs)
#print(t)
yield t, te
except KeyError:
print(tc.red('WARNING:'), 'could not find', ontology, 'in import chain') # TODO zap onts w/o imports
def new_index(self, referenceIndex, *, commit=True):
""" reference hosts have a single incrementing primary key index
to which everything is mapped
in theory these indexes could also be per 'prefix' aka
the sandboxed uri path or external uri path to which
something is mapped I don't see any reason not to do this
for this kind of implementation since a regular pattern
can be develop
"""
'''
QUESTION: do we force a remapping of external id sequences
into uris/ first? this seems like a bad idea? or rather,
it is actually a good idea, but it will have to be done with
a pattern based redirect instead of an actual materialization
the alternative is to do what ontobee does and pass the external
iri as a query parameter ... hrm tradoffs, well we certainly
can't make a nice /uberon/uris/obo/{UBERON_} folder if we include
the whole uri ... so this seems a reasonable tradeoff
http://purl.obolibrary.org/obo/ can wind up being mapped into
multiple uri spaces ... /obo/uris/obo/ would seem to make more sense
but how to indicate that other organizations/projects map there ...
/uberon/uris/obo/UBERON_ could indicate the latest sequence
ah, and of course in theory this gets us out of the very annoying
situation where /uberon/uris/obo/UBERON_ really IS different than
/doid/uris/obo/UBERON_ for some identifiers (sigh) and if they are
all mapped and masking based on presence then we can detect the issues
HOWEVER how do we enforce that in reality the _mapping_ is all to
/obo/uris/obo/ ??
'''
path = self.path_index(referenceIndex)
rrp = path.repo_relative_path
s = sncho[rrp.with_suffix('').as_posix()] # TODO check ownership
if path.exists():
raise FileExistsError(path)
g = OntGraph(path=path)
OntCuries.populate(g)
# TODO these are really identified by the follow:
# base/readable/
# {group}/uris/
# base/ontologies/
# {group}/ontologies/uris/
pos = (
(rdf.type, snchn.IndexGraph),
(rdfs.label, rdflib.Literal(f'IndexGraph for {referenceIndex}')),
(snchn.referenceIndex, rdflib.Literal(referenceIndex)), # TODO HRM
#(snchn.indexRemote, )
)
for po in pos:
g.add((s, *po)) # FIXME
g.path.parent.mkdir(parents=True)
g.write()
if commit:
path.commit(f'add new index for {referenceIndex}')
return path