def get_exact_matches_to_concept_list(c):
response = []
for curie in c:
if not isinstance(curie, str) or ':' not in curie:
continue
exact_matches = []
data = crawler.crawl(curie)
for category, associations in data.items():
for a in associations:
if a.get('predicate') == 'EquivalentAssociation':
object_id = safe_get(a, 'object', 'id')
prefix, local_id = object_id.split(':', 1)
if 'name' not in prefix.lower():
exact_matches.append(object_id)
response.append(
ExactMatchResponse(id=curie,
within_domain=data != {},
has_exact_matches=exact_matches))
return response
def get_statement_details(statementId, keywords=None, offset=None, size=None):
if ':' not in statementId:
return BeaconStatementWithDetails()
p = statementId.split(':')
if len(p) != 5:
return BeaconStatementWithDetails()
subject_id = '{}:{}'.format(p[0], p[1])
predicate = '{}'.format(p[2])
object_id = '{}:{}'.format(p[3], p[4])
data = crawler.crawl(subject_id)
for category, assocations in data.items():
for a in assocations:
object_match = object_id == simplify_curie(
safe_get(a, 'object', 'id'))
predicate_match = predicate == safe_get(a, 'predicate')
edge_label = safe_get(a, 'edge', 'label')
if edge_label is not None:
edge_label = edge_label.replace(' ', '_')
predicate = predicate.replace(' ', '_')
label_match = predicate == edge_label
if object_match and (label_match or predicate_match):
provided_by = safe_get(a, 'edge', 'provided_by')
probability = safe_get(a, 'edge', 'probability')
predicate = safe_get(a, 'predicate')
is_defined_by = safe_get(a, 'api')
endpoint = safe_get(a, 'endpoint')
annotations = []
if probability is not None:
annotations.append(
BeaconStatementAnnotation(tag='probability',
value=probability))
if predicate is not None:
annotations.append(
BeaconStatementAnnotation(tag='predicate',
value=predicate))
if endpoint is not None:
annotations.append(
BeaconStatementAnnotation(tag='endpoint',
value=endpoint))
annotations.append(
BeaconStatementAnnotation(tag='endpoint_input',
value=subject_id))
return BeaconStatementWithDetails(provided_by=provided_by,
is_defined_by=is_defined_by,
annotation=annotations)
return BeaconStatementWithDetails()
def get_concept_details(conceptId):
data = crawler.crawl(conceptId)
if data == {}:
return BeaconConceptWithDetails()
names, descriptions, xrefs = [], [], []
for category, associations in data.items():
for a in associations:
predicate = a.get('predicate')
if predicate == 'EquivalentAssociation' or predicate == 'HasDescriptionAssociation':
object_id = safe_get(a, 'object', 'id')
prefix, local_id = object_id.split(':', 1)
if 'name' in prefix.lower() or 'symbol' in prefix.lower():
names.append(local_id)
if 'description' in prefix.lower():
descriptions.append(local_id)
if not 'name' in prefix.lower(
) and not 'description' in prefix.lower():
xrefs.append(object_id)
names = list(set(names))
predicate_longest_under_sixty = lambda n: (len(n) > 60, -len(n))
names.sort(key=predicate_longest_under_sixty)
prefix, _ = conceptId.split(':', 1)
c = BeaconConceptWithDetails(id=conceptId,
name=names[0] if len(names) >= 1 else None,
synonyms=names[1:],
exact_matches=xrefs,
categories=[lookup_category(prefix)],
description='; '.join(descriptions))
return c
def get_statements(s=None,
s_keywords=None,
s_categories=None,
edge_label=None,
relation=None,
t=None,
t_keywords=None,
t_categories=None,
offset=None,
size=None):
if s is None:
abort(400,
'Cannot search for statements without providing a subject ID')
statements = []
for subject_id in s:
if ':' not in subject_id:
continue
data = crawler.crawl(subject_id)
if data == {}:
continue
subject_name = find_subject_name(data)
for category, associations in data.items():
if category == 'null':
category = None
for a in associations:
object_id = safe_get(a, 'object', 'id')
if object_id != None and ':' in object_id:
object_prefix, _ = object_id.split(':', 1)
object_prefix = object_prefix.lower()
if 'name' in object_prefix or 'description' in object_prefix:
continue
object_name = safe_get(a, 'object', 'label')
if object_name == None:
secondary_id = safe_get(a, 'object', 'secondary-id')
if secondary_id != None and ':' in secondary_id:
secondary_prefix, symbol = secondary_id.split(':', 1)
object_name = symbol
if 'symbol' in secondary_prefix.lower():
taxonomy = safe_get(a, 'object', 'taxonomy')
if taxonomy != None:
taxonomy = ', '.join(t for t in taxonomy
if ':' not in t)
object_name += ' (taxonomy: {})'.format(
taxonomy)
subject_prefix, _ = subject_id.split(':', 1)
predicate_name = safe_get(a, 'edge', 'label')
if predicate_name == None:
predicate_name = safe_get(a, 'predicate')
if predicate_name == 'EquivalentAssociation':
predicate_name = 'same_as'
if isinstance(predicate_name, list):
if predicate_name != []:
predicate_name = predicate_name[0]
else:
predicate_name = blm.DEFAULT_EDGE_LABEL
predicate_name = predicate_name.replace(' ', '_')
object_id = simplify_curie(object_id)
subject_id = simplify_curie(subject_id)
statements.append(
build_statement(
object_id=object_id,
object_name=object_name,
object_category=category,
subject_id=subject_id,
subject_name=subject_name,
subject_category=utils.lookup_category(subject_prefix),
predicate_id=safe_get(a, 'edge', 'id'),
predicate_name=predicate_name))
is_valid = build_filter(s, s_keywords, s_categories, edge_label, relation,
t, t_keywords, t_categories)
statements = [s for s in statements if is_valid(s)]
statements = remove_duplicates(statements)
if offset is not None:
statements = statements[offset:]
if size is not None:
statements = statements[:size]
return statements