def setUp(self):
ontquery.OntCuries(core.PREFIXES)
#self.query = OntQuery(localonts, remoteonts1, remoteonts2) # provide by default maybe as ontquery?
#bs = ontquery.BasicService() # TODO
#self.query = ontquery.OntQuery(bs, upstream=OntTerm)
if 'SCICRUNCH_API_KEY' in os.environ:
self.query = ontquery.OntQuery(
ontquery.SciGraphRemote(api_key=core.get_api_key()),
upstream=OntTerm)
else:
self.query = ontquery.OntQuery(ontquery.SciGraphRemote(
apiEndpoint='http://localhost:9000/scigraph'),
upstream=OntTerm)
def setup(self, **kwargs):
oq.OntCuries({'TMP': 'http://uri.interlex.org/base/tmp_'})
if self.apiEndpoint is not None:
try:
self.ilx_cli = InterLexClient(base_url=self.apiEndpoint)
except exc.NoApiKeyError:
if not self.readonly:
# expect attribute errors for ilx_cli
log.warning(
'You have not set an API key for the SciCrunch API! '
'InterLexRemote will error if you try to use it.')
super().setup(**kwargs)
def setUp(self):
#self.query = oq.OntQuery(localonts, remoteonts1, remoteonts2) # provide by default maybe as oq?
#bs = oq.BasicService() # TODO
#self.query = oq.OntQuery(bs, upstream=OntTerm)
#oq.QueryResult._OntTerm = OntTerm
SCR = oq.plugin.get('SciCrunch')()
services = SCR,
# this was an ok idea, but better to also have known good local prefixes
# probably need to clean up an clarify the bad old
#services[0].setup() # explicit call to setup so we can populate OntCuries
#oq.OntCuries(services[0].curies)
oq.OntCuries(CURIE_MAP)
self.query = oq.OntQueryCli(*services, instrumented=OntTerm)
oq.OntTerm.query_init(*services)
oq.utils.log.setLevel('DEBUG')
log = oq.utils.log.getChild('test')
try:
from pyontutils.namespaces import PREFIXES as CURIE_MAP
from pyontutils import scigraph
except ModuleNotFoundError:
from ontquery.plugins.services import scigraph_client as scigraph
from ontquery.plugins.namespaces.nifstd import CURIE_MAP
SKIP_NETWORK = ('SKIP_NETWORK' in os.environ or 'FEATURES' in os.environ
and 'network-sandbox' in os.environ['FEATURES'])
skipif_no_net = pytest.mark.skipif(
SKIP_NETWORK, reason='Skipping due to network requirement')
oq.OntCuries(CURIE_MAP)
suffixes = (
'',
'hello',
'world',
'ev:il',
'1234567',
'1232/123123/asdfasdf',
'lol_this#is/even-worse/_/123',
)
test_graph = rdflib.Graph()
triples = (
('UBERON:0000955', 'rdf:type', 'owl:Class'),
('UBERON:0000955', 'rdfs:label', 'brain'),
import os
import unittest
from uuid import uuid4
import pytest
import rdflib
import ontquery as oq
from .common import test_graph, skipif_no_net, log
from .test_interlex_client import skipif_no_api_key
# FIXME TODO per service ... + mismatch warning
oq.OntCuries({
'rdf': str(rdflib.RDF),
'rdfs': str(rdflib.RDFS),
'owl': str(rdflib.OWL),
'BFO': 'http://purl.obolibrary.org/obo/BFO_',
'UBERON': 'http://purl.obolibrary.org/obo/UBERON_',
'NLX': 'http://uri.neuinfo.org/nif/nifstd/nlx_',
'BIRNLEX': 'http://uri.neuinfo.org/nif/nifstd/birnlex_',
'ILX': 'http://uri.interlex.org/base/ilx_',
'RO': 'http://purl.obolibrary.org/obo/RO_',
'hasRole': 'http://purl.obolibrary.org/obo/RO_0000087',
})
oq.OntCuries({
'hasPart': oq.OntId('BFO:0000051'),
'partOf': oq.OntId('BFO:0000050'),
})
OntId = oq.OntId
class ServiceBase:
def setUp(self):
class OntTerm(oq.OntTerm):
def setUp(self):
oq.OntCuries(common.CURIE_MAP)