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Merge pull request #408 from biolink/direct-inferred-19112019
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Support for querying for direct vs inferred associations, other fixes for ui
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@kshefchek
kshefchek authored Jan 13, 2020
2 parents f921041 + 1ff187b commit 878d94f
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Showing 3 changed files with 98 additions and 69 deletions.
155 changes: 92 additions & 63 deletions ontobio/golr/golr_query.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -840,8 +840,11 @@ def __init__(self,
object=None,
objects=None,
subject_direct=False,
object_direct=False,
subject_taxon=None,
subject_taxon_direct=False,
object_taxon=None,
object_taxon_direct=False,
invert_subject_object=None,
evidence=None,
exclude_automatic_assertions=False,
Expand Down Expand Up @@ -884,57 +887,60 @@ def __init__(self,
"""
self.subject_category=subject_category
self.object_category=object_category
self.relation=relation
self.relationship_type=relationship_type
self.subject_or_object_ids=subject_or_object_ids
self.subject_or_object_category=subject_or_object_category
self.subject=subject
self.subjects=subjects
self.object=object
self.objects=objects
self.subject_direct=subject_direct
self.subject_taxon=subject_taxon
self.object_taxon=object_taxon
self.invert_subject_object=invert_subject_object
self.evidence=evidence
self.exclude_automatic_assertions=exclude_automatic_assertions
self.id=id
self.q=q
self.use_compact_associations=use_compact_associations
self.include_raw=include_raw
self.field_mapping=field_mapping
self.solr=solr
self.subject_category = subject_category
self.object_category = object_category
self.relation = relation
self.relationship_type = relationship_type
self.subject_or_object_ids = subject_or_object_ids
self.subject_or_object_category = subject_or_object_category
self.subject = subject
self.subjects = subjects
self.subject_direct = subject_direct
self.object = object
self.objects = objects
self.object_direct = object_direct
self.subject_taxon = subject_taxon
self.subject_taxon_direct = subject_taxon_direct
self.object_taxon = object_taxon
self.object_taxon_direct = object_taxon_direct
self.invert_subject_object = invert_subject_object
self.evidence = evidence
self.exclude_automatic_assertions = exclude_automatic_assertions
self.id = id
self.q = q
self.use_compact_associations = use_compact_associations
self.include_raw = include_raw
self.field_mapping = field_mapping
self.solr = solr
self.config = config
self.select_fields=select_fields
self.fetch_objects=fetch_objects
self.fetch_subjects=fetch_subjects
self.fq=fq if fq is not None else {}
self.select_fields = select_fields
self.fetch_objects = fetch_objects
self.fetch_subjects = fetch_subjects
self.fq = fq if fq is not None else {}
self.slim = slim if slim is not None else []
self.json_facet=json_facet
self.iterate=iterate
self.map_identifiers=map_identifiers
self.facet_fields=facet_fields
self.facet_field_limits=facet_field_limits
self.facet_limit=facet_limit
self.facet_mincount=facet_mincount
self.facet_pivot_fields=facet_pivot_fields
self.stats=stats
self.stats_field=stats_field
self.facet=facet
self.pivot_subject_object=pivot_subject_object
self.unselect_evidence=unselect_evidence
self.max_rows=100000
self.rows=rows
self.start=start
self.json_facet = json_facet
self.iterate = iterate
self.map_identifiers = map_identifiers
self.facet_fields = facet_fields
self.facet_field_limits = facet_field_limits
self.facet_limit = facet_limit
self.facet_mincount = facet_mincount
self.facet_pivot_fields = facet_pivot_fields
self.stats = stats
self.stats_field = stats_field
self.facet = facet
self.pivot_subject_object = pivot_subject_object
self.unselect_evidence = unselect_evidence
self.max_rows = 100000
self.rows = rows
self.start = start
self.homology_type = homology_type
self.url = url
# test if client explicitly passes a URL; do not override
self.is_explicit_url = url is not None
self.non_null_fields=non_null_fields
self.association_type=association_type
self.sort=sort
self.non_null_fields = non_null_fields
self.association_type = association_type
self.sort = sort

self.user_agent = get_user_agent(modules=[requests, pysolr], caller_name=__name__)
if user_agent is not None:
Expand Down Expand Up @@ -994,18 +1000,22 @@ def solr_params(self):
#if subject is not None and subject.startswith('MGI:MGI:'):
# logging.info('Unhacking MGI ID presumably from GO:'+str(subject))
# subject = subject.replace("MGI:MGI:","MGI")
subject=self.subject
subject = self.subject
if subject is not None:
subject = self.make_canonical_identifier(subject)
subjects=self.subjects
subjects = self.subjects
if subjects is not None:
subjects = [self.make_canonical_identifier(s) for s in subjects]

subject_direct = self.subject_direct

# temporary: for querying go solr, map fields. TODO
object_category=self.object_category
object_category = self.object_category
logging.info("Object category: {}".format(object_category))

object=self.object
object = self.object
objects = self.objects
object_direct = self.object_direct
if object_category is None and object is not None and object.startswith('GO:'):
# Infer category
object_category = 'function'
Expand Down Expand Up @@ -1041,8 +1051,9 @@ def solr_params(self):
object = cc

## subject params
subject_taxon=self.subject_taxon
subject_category=self.subject_category
subject_taxon = self.subject_taxon
subject_taxon_direct = self.subject_taxon_direct
subject_category = self.subject_category

# heuristic procedure to guess unspecified subject_category
if subject_category is None and subject is not None:
Expand All @@ -1067,13 +1078,16 @@ def solr_params(self):

## taxon of object of triple
object_taxon=self.object_taxon
object_taxon_direct = self.object_taxon_direct

# typically information is stored one-way, e.g. model-disease;
# sometimes we want associations from perspective of object
if self.invert_subject_object:
(subject,object) = (object,subject)
(subject_category,object_category) = (object_category,subject_category)
(subject_taxon,object_taxon) = (object_taxon,subject_taxon)
(subject, object) = (object,subject)
(subject_category, object_category) = (object_category,subject_category)
(subject_taxon, object_taxon) = (object_taxon,subject_taxon)
(object_direct, subject_direct) = (subject_direct, object_direct)
(object_taxon_direct, subject_taxon_direct) = (subject_taxon_direct, object_taxon_direct)

## facet fields
facet_fields=self.facet_fields
Expand All @@ -1096,24 +1110,32 @@ def solr_params(self):
if object_category is not None:
fq['object_category'] = object_category


if object is not None:
# TODO: make configurable whether to use closure
fq['object_closure'] = object
if subject is not None:
# note: by including subject closure by default,
# we automaticaly get equivalent nodes
if self.subject_direct:
fq['subject'] = subject
if subject_direct:
fq['subject_eq'] = subject
else:
fq['subject_closure'] = subject
if subjects is not None:
# lists are assumed to be disjunctive
if self.subject_direct:
if subject_direct:
fq['subject'] = subjects
else:
fq['subject_closure'] = subjects

if object is not None:
if object_direct:
fq['object_eq'] = object
else:
fq['object_closure'] = object
if objects is not None:
# lists are assumed to be disjunctive
if object_direct:
fq['object_eq'] = objects
else:
fq['object_eq'] = objects

objects=self.objects
if objects is not None:
# lists are assumed to be disjunctive
Expand All @@ -1122,9 +1144,16 @@ def solr_params(self):
if relation is not None:
fq['relation_closure'] = relation
if subject_taxon is not None:
fq['subject_taxon_closure'] = subject_taxon
if subject_taxon_direct:
fq['subject_taxon'] = subject_taxon
else:
fq['subject_taxon_closure'] = subject_taxon
if object_taxon is not None:
fq['object_taxon_closure'] = object_taxon
if object_taxon_direct:
fq['object_taxon'] = object_taxon
else:
fq['object_taxon_closure'] = object_taxon

if self.id is not None:
fq['id'] = self.id
if self.evidence is not None:
Expand Down
8 changes: 3 additions & 5 deletions ontobio/sim/api/owlsim2.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ def search_by_attribute_set(
'limit': limit,
'target': namespace_filter
}
return requests.get(owlsim_url, params=params, timeout=TIMEOUT).json()
return requests.post(owlsim_url, data=params, timeout=TIMEOUT).json()


@cache.memoize()
Expand All @@ -71,9 +71,7 @@ def compare_attribute_sets(
'b': profile_b,
}

print(requests.get(owlsim_url, params=params, timeout=TIMEOUT).json())

return requests.get(owlsim_url, params=params, timeout=TIMEOUT).json()
return requests.post(owlsim_url, data=params, timeout=TIMEOUT).json()


@cache.memoize()
Expand All @@ -100,7 +98,7 @@ def get_attribute_information_profile(
'a': profile,
'r': categories
}
return requests.get(owlsim_url, params=params, timeout=TIMEOUT).json()
return requests.post(owlsim_url, data=params, timeout=TIMEOUT).json()


@cache.memoize()
Expand Down
4 changes: 3 additions & 1 deletion ontobio/util/scigraph_util.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def get_scigraph_nodes(id_list)-> Iterator[Dict]:
"""
scigraph = RemoteScigraphOntology('scigraph:data')

chunks = [id_list[i:i + 400] for i in range(0, len(list(id_list)), 400)]
chunks = [id_list[i:i + 100] for i in range(0, len(list(id_list)), 100)]
for chunk in chunks:
params = {
'id': chunk,
Expand Down Expand Up @@ -95,6 +95,8 @@ def get_id_type_map(id_list: Iterable[str]) -> Dict[str, List[str]]:
for node in get_scigraph_nodes(id_list):
type_map[node['id']] = [typ.lower() for typ in node['meta']['types']
if typ not in filter_out_types]
if not type_map[node['id']]:
type_map[node['id']] = ['Node']

return type_map

Expand Down

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