import requests
import warnings
import re
import json
from ..default_servers import get_default_servers
[docs]class OWLeryConnect:
"""Wrapper class for querying the VFB OWLery endpoint.
Unless you have specialist configuration needs, it is
better to access this object with full default configurations
from VfbConnect.oc.
:param endpoint: owlery REST endpoint
:param lookup: Dict of name: ID;
:param: obo_curies: list of prefixes for generation of OBO curies.
Default: ('FBbt', 'RO')
:param: curies: Dict of curies"""
def __init__(self,
endpoint=get_default_servers()['owlery_endpoint'],
lookup=None,
obo_curies=('FBbt', 'RO', 'BFO'),
curies=None):
self.owlery_endpoint = endpoint
if not (lookup):
self.lookup = {}
else:
self.lookup = lookup
if not curies:
self.curies = {}
else:
self.curies = curies
if obo_curies:
self._add_obo_curies(obo_curies)
def _add_obo_curies(self, prefixes):
obolib = "http://purl.obolibrary.org/obo/"
c = {p : obolib + p + '_' for p in prefixes}
self.curies.update(c)
[docs] def query(self, query_type, return_type,
query, query_by_label=False, direct=False, verbose=False):
"""
A wrapper for querying Owlery Endpoints. See
https://owlery.phenoscape.org/api/ for doc
:param query_type: Options: subclasses, superclasses,
equivalent, instances, types
:param query: 'Manchester syntax query with owl entities as <iri>,
curie (supporting curies declared on object)
or single quoted label (if query_by_label isTrue)
:param query_by_label: Boolean. Default False.
:param direct: Boolean. Default False. Determines T/F
:param verbose - print verbose output to stdout for debugging purposes.
:return: list of IRIs.
"""
owl_endpoint = self.owlery_endpoint + query_type +"?"
if query_by_label:
query = self.labels_2_ids(query)
print("Running query: " + query)
payload = {'object': query, 'prefixes': json.dumps(self.curies),
'direct': direct}
# print(payload)
r = requests.get(url=owl_endpoint, params=payload)
print("Query URL: " + r.url)
if r.status_code == 200:
print("Query results: " + str(len(r.json()[return_type])))
return r.json()[return_type]
else:
warnings.warn(str(r.content))
return False
[docs] def get_subclasses(self, query, query_by_label=False, direct=False, return_short_forms=False):
"""Generate list of IDs of all subclasses of class_expression.
:param class_expression: A valid OWL class expression, e.g. the name of a class.
:param query_by_label: Optional. If `False``, class_expression takes CURIEs instead of labels. Default `False`
:param direct: Return direct subclasses only. Default `False`
:param return_short_forms: Optional. If `True`, returns short_forms instead of IRIs.
:return: Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
:rtype: list of IRIs or short_forms (depending on return_short_form option)
"""
out = self.query(query_type='subclasses', return_type='superClassOf',
query=query, query_by_label=query_by_label,
direct=direct)
if return_short_forms:
return list(map(gen_short_form, out))
else:
return out
[docs] def get_instances(self, query, query_by_label=False, direct=False, return_short_forms=False):
"""Generate list of IDs of all instances of class_expression.
:param class_expression: A valid OWL class expression, e.g. the name of a class.
:param query_by_label: Optional. If `False``, class_expression takes CURIEs instead of labels. Default `False`
:param direct: Return direct instances only. Default `False`
:param return_short_forms: Optional. If `True`, returns short_forms instead of IRIs.
:return: Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
:rtype: list of IRIs or short_forms (depending on return_short_form option)
"""
out = self.query(query_type='instances', return_type='hasInstance',
query=query, query_by_label=query_by_label,
direct=direct)
if return_short_forms:
return list(map(gen_short_form, out))
else:
return out
[docs] def get_superclasses(self, query, query_by_label=False, direct=False, return_short_forms=False):
"""Generate list of IDs of all superclasses of class_expression.
:param class_expression: A valid OWL class expression, e.g. the name (or CURIE) of a class.
:param query_by_label: Optional. If `False``, class_expression takes CURIEs instead of labels. Default `False`
:param direct: Return direct instances only. Default `False`
:param return_short_forms: Optional. If `True`, returns short_forms instead of IRIs.
:return: Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
:rtype: list of IRIs or short_forms (depending on return_short_form option)
"""
out = self.query(query_type='superclasses', return_type='subClassOf',
query=query, query_by_label=query_by_label,
direct=direct)
if return_short_forms:
return list(map(gen_short_form, out))
else:
return out
[docs] def labels_2_ids(self, query_string):
"""Substitutes labels for IDs in a query string
:param query_string: A OWL class expression in which all labels of OWL entities are single-quoted. Internal
single quotes should be escaped with a backslash.
:return: query string in which labels have been converted to unquoted CURIES.
"""
def subgp1_or_fail(m):
out = self.lookup.get(m.group(1))
if not out:
raise ValueError("Query includes unknown term label: " + query_string)
else:
return out
# This doesn't deal well with failure -> lambda too separate function
return re.sub(r"'(.+?)'", lambda m: subgp1_or_fail(m), query_string)