def setup(self, **kwargs):
self.sgv = scigraph.Vocabulary(cache=self.cache,
verbose=self.verbose,
basePath=self.apiEndpoint,
safe_cache=True)
self.sgg = scigraph.Graph(cache=self.cache,
verbose=self.verbose,
basePath=self.apiEndpoint)
self.sgc = scigraph.Cypher(cache=self.cache,
verbose=self.verbose,
basePath=self.apiEndpoint)
self.sgd = scigraph.Dynamic(cache=self.cache,
verbose=self.verbose,
basePath=self.apiEndpoint)
self.curies = type('LocalCuries', (oq.OntCuries, ), {})
self._remote_curies = type('RemoteCuries', (oq.OntCuries.new(), ), {})
curies = self.sgc.getCuries()
self.curies(curies) # TODO can be used to provide curies...
self._remote_curies(curies)
self.prefixes = sorted(self.curies)
self.search_prefixes = [
p for p in sorted(self._remote_curies) if p != 'SCR'
]
self.categories = self.sgv.getCategories()
self._predicates = sorted(set(self.sgg.getRelationships()))
#self._onts = sorted(o['n']['iri'] for o in self.sgc.execute('MATCH (n:Ontology) RETURN n', 1000, 'application/json')) # only on newer versions, update when we switch production over
self._onts = sorted(o['iri'] for o in self.sgc.execute(
'MATCH (n:Ontology) RETURN n', 1000, 'text/plain'))
super().setup(**kwargs)
dematerialize,
flatten as flatten_tree)
from pyontutils.namespaces import rdfs, OntCuries
from pyontutils.scigraph_codegen import moduleDirect
from nifstd_tools.sheets_sparc import (hyperlink_tree,
tag_row,
open_custom_sparc_view_yml,
YML_DELIMITER)
from nifstd_tools.simplify import simplify, cleanBad
from nifstd_tools import __version__
log = makeSimpleLogger('ontree')
# FIXME these will go to network which is :/
sgg = scigraph.Graph(cache=False, verbose=True)
sgv = scigraph.Vocabulary(cache=False, verbose=True)
sgc = scigraph.Cypher(cache=False, verbose=True)
sgd = scigraph.Dynamic(cache=False, verbose=True)
# This was for ttl creation extension for sparc view
# ixr.setup(instrumented=OntTerm)
a = 'rdfs:subClassOf'
_hpp = 'RO_OLD:has_proper_part' # and apparently this fails too
hpp = 'http://www.obofoundry.org/ro/ro.owl#has_proper_part'
hpp = 'NIFRID:has_proper_part'
po = 'BFO:0000050' # how?! WHY does this fail!? the curie is there!
_po = 'http://purl.obolibrary.org/obo/BFO_0000050'
hr = 'RO:0000087'
_hr = 'http://purl.obolibrary.org/obo/RO_0000087'