In past 2 weeks, I tried to use Ontology Factory several time but in first cell ontology object is not initializing.
from ontobio.ontol_factory import OntologyFactory
ofa = OntologyFactory()
ont = ofa.create('go')
It takes a-lot of time even hours but it does not initialize. I think there is something wrong on server side. On interrupting kernel of Notebook I found the following error. Last passage of error kept repeating again and again.
Please check server side if it is ok please guide me why it is not working now even it was working few days ago. Thanks in advance for your time and help.

---

KeyboardInterrupt Traceback (most recent call last)
in ()
3 from ontobio.ontol_factory import OntologyFactory
4 ofa = OntologyFactory()
----> 5 ont = ofa.create('go')

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\ontol_factory.py in create(self, handle, **args)
74 logging.info("Using default_ontology")
75 return default_ontology
---> 76 return create_ontology(handle, **args)
77
78 #@cachier(stale_after=SHELF_LIFE)

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\ontol_factory.py in create_ontology(handle, **args)
126 else:
127 logging.info("Fetching from SPARQL")
--> 128 ont = EagerRemoteSparqlOntology(handle=handle)
129 #g = get_digraph(handle, None, True)
130 return ont

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\sparql\sparql_ontology.py in init(self, handle)
171 self.graph = g
172 self.graph_name = get_named_graph(handle)
--> 173 self.xref_graph = get_xref_graph(handle)
174 self.all_logical_definitions = []
175 logging.info("Graph: {} LDs: {}".format(self.graph, self.all_logical_definitions))

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\sparql\sparql_ontol_utils.py in get_xref_graph(ont)
64 """
65 g = networkx.MultiGraph()
---> 66 for (c,x) in fetchall_xrefs(ont):
67 g.add_edge(c,x,source=c)
68 return g

C:\Users\Badar Khan\Anaconda3\lib\site-packages\cachier\core.py in func_wrapper(*args, **kwds)
157 return entry['value'] # return stale val
158 _print('Already calc. Waiting on change.')
--> 159 return core.wait_on_entry_calc(key)
160 if next_time:
161 _print('Async calc and return stale')

C:\Users\Badar Khan\Anaconda3\lib\site-packages\cachier\pickle_core.py in wait_on_entry_calc(self, key)
191 if observer.isAlive():
192 # print('Timedout waiting. Starting again...')
--> 193 return self.wait_on_entry_calc(key)
194 # print("Returned value: {}".format(event_handler.value))
195 return event_handler.value

C:\Users\Badar Khan\Anaconda3\lib\site-packages\cachier\pickle_core.py in wait_on_entry_calc(self, key)
191 if observer.isAlive():
192 # print('Timedout waiting. Starting again...')
--> 193 return self.wait_on_entry_calc(key)
194 # print("Returned value: {}".format(event_handler.value))
195 return event_handler.value

Let's populate this repo with more examples!

Some could be adapted from: https://nbviewer.jupyter.org/github/biolink/ontobio/tree/master/notebooks/

Hi,
I ran this code but found error in 2nd cell. Please guide me what is its cause.
For reference Code and its detail is attached. Ontobio package is added successfully.

Code of 2nd Cell

-Create an association factory to get pombase GO annotations
-(this uses an 'eager' method, where all annotations are fetched from services in advance)
from ontobio.assoc_factory import AssociationSetFactory
afactory = AssociationSetFactory()
aset = afactory.create(ontology=ont, subject_category='gene', object_category='function', taxon='NCBITaxon:4896')

Error of 2nd Cell

---

AttributeError Traceback (most recent call last)
in ()
3 from ontobio.assoc_factory import AssociationSetFactory
4 afactory = AssociationSetFactory()
----> 5 aset = afactory.create(ontology=ont, subject_category='gene', object_category='function', taxon='NCBITaxon:4896')

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\assoc_factory.py in create(self, ontology, subject_category, object_category, evidence, taxon, relation, file, fmt)
60 object_category=object_category,
61 evidence=evidence,
---> 62 taxon=taxon)
63
64 logging.info("Creating map for {} subjects".format(len(assocs)))

C:\Users\Badar Khan\Anaconda3\lib\site-packages\cachier\core.py in func_wrapper(*args, **kwds)
176 return core.wait_on_entry_calc(key)
177 _print('No entry found. No current calc. Calling like a boss.')
--> 178 return _calc_entry(core, key, func, args, kwds)
179
180 def clear_cache():

C:\Users\Badar Khan\Anaconda3\lib\site-packages\cachier\core.py in _calc_entry(core, key, func, args, kwds)
76 core.mark_entry_being_calculated(key)
77 # _get_executor().submit(core.mark_entry_being_calculated, key)
---> 78 func_res = func(*args, **kwds)
79 core.set_entry(key, func_res)
80 # _get_executor().submit(core.set_entry, key, func_res)

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\assoc_factory.py in bulk_fetch_cached(**args)
150 def bulk_fetch_cached(**args):
151 logging.info("Fetching assocs from store (will be cached)")
--> 152 return bulk_fetch(**args)
153

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\golr\golr_associations.py in bulk_fetch(subject_category, object_category, taxon, rows, **kwargs)
144 rows=rows,
145 iterative=True,
--> 146 **kwargs)
147 logging.info("Rows retrieved: {}".format(len(assocs)))
148 if len(assocs) == 0:

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\golr\golr_associations.py in search_associations_compact(**kwargs)
75 searchresult = search_associations(use_compact_associations=True,
76 facet_fields=[],
---> 77 **kwargs
78 )
79 return searchresult['compact_associations']

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\golr\golr_associations.py in search_associations(**kwargs)
31 logging.info("CREATING_GOLR_QUERY {}".format(kwargs))
32 q = GolrAssociationQuery(**kwargs)
---> 33 return q.exec()
34
35 def get_objects_for_subject(subject=None,

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\golr\golr_query.py in exec(self, **kwargs)
830 """
831
--> 832 params = self.solr_params()
833 logging.info("PARAMS="+str(params))
834 results = self.solr.search(**params)

C:\Users\Badar Khan\Anaconda3\lib\site-packages\ontobio\golr\golr_query.py in solr_params(self)
560 if self.solr is None:
561 if self.url is None:
--> 562 self._set_solr(self.get_config().solr_assocs)
563 #self.solr = monarch_solr
564 else:

AttributeError: 'Session' object has no attribute 'solr_assocs'