def get(self, term):
"""
Returns list of matching concepts or entities using lexical search
"""
args = simple_parser.parse_args()
q = GolrSearchQuery(term, user_agent=USER_AGENT, **args)
results = q.search()
return results
def get(self, term):
"""
Returns list of matching concepts or entities using lexical search
"""
args = simple_parser.parse_args()
q = GolrSearchQuery(term, **args)
results = q.autocomplete()
return results
def get(self, term):
"""
Returns list of matching concepts or entities using lexical search
"""
args = simple_parser.parse_args()
args['fq_string'] = copy.copy(args['fq'])
args['fq'] = {}
q = GolrSearchQuery(term, user_agent=USER_AGENT, **args)
results = q.autocomplete()
return results
def setup_class(self):
self.manager = GolrSearchQuery()
# Mock the PySolr search function to
# return our test docs
input_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/solr-docs.json')
input_docs = json.load(open(input_fh))
self.test_results = pysolr.Results(input_docs)
self.manager.solr.search = MagicMock(return_value=self.test_results)
def test_search_go_ontol():
q = GolrSearchQuery("transport*", category='ontology_class', is_go=True)
print("Q={}".format(q))
params = q.solr_params()
print("PARAMS={}".format(params))
results = q.exec()
print("RESULTS={}".format(results))
docs = results['docs']
for r in docs:
print(str(r))
assert len(docs) > 0
def test_search():
q = GolrSearchQuery("abnormal")
print("Q={}".format(q))
params = q.solr_params()
print("PARAMS={}".format(params))
results = q.exec()
print("RESULTS={}".format(results))
docs = results['docs']
for r in docs:
print(str(r))
assert len(docs) > 0
def test_search_go_all():
q = GolrSearchQuery("transport*", is_go=True)
print("Q={}".format(q))
params = q.solr_params()
print("PARAMS={}".format(params))
results = q.exec()
print("RESULTS={}".format(results))
docs = results['docs']
for r in docs:
print(str(r))
assert len(docs) > 0
print(str(results['facet_counts']))
def clean_feature_ids(id: str) -> str:
"""
MME queries often need to be sanitized before going into owlsim, for example:
MIM:610536 -> OMIM:610536
SHH -> HGNC:10848
"""
if ':' in id:
prefix, reference = id.split(':')
if prefix == 'MIM':
id = 'OMIM:' + reference
else:
# Assume it's a label and look it up
# Assume it's human, and make sure it's an exact match
query = GolrSearchQuery(id, taxon=['NCBITaxon:9606'], min_match="100%")
results = query.search()
if results.docs:
id = results.docs[0]['id']
return id
def get_concepts():
keywords = request.args.get('keywords', None)
semanticGroups = request.args.get('semanticGroups', None)
pageSize = int(request.args.get('pageSize', 1))
pageNumber = int(request.args.get('pageNumber', 1))
validatePagination(pageSize, pageNumber)
validateKeywords(keywords)
q = GolrSearchQuery(term=keywords,
category=build_categories(semanticGroups),
rows=pageSize,
start=getStartIndex(pageNumber, pageSize))
results = q.exec()
concepts = []
for d in results['docs']:
concept = parse_concept(d)
concepts.append(concept)
return jsonify(concepts)
def get_concept(conceptId):
if conceptId.startswith("biolink"):
conceptId = objectId(conceptId)
results = GolrSearchQuery(term=conceptId,
fq={
'id': conceptId
},
rows=1,
hl=False).exec()
c = None
entries = []
for d in results['docs']:
c = parse_concept(d)
break
return c
def find_exactmatches(conceptId):
"""
Returns a list of concept ID's that are exact matches for the given conceptId
"""
results = GolrSearchQuery(term=conceptId,
fq={
'id': conceptId
},
rows=1,
hl=False).exec()
docs = results['docs']
for d in docs:
if get_concept_property(d, 'id') == conceptId:
exactmatches = get_concept_property(d, 'equivalent_curie')
if exactmatches == None:
exactmatches = [] # just in case this property is empty
exactmatches.append(conceptId)
return exactmatches if exactmatches != None else []
return []
def get_concept_details(conceptId):
if conceptId.startswith("biolink"):
conceptId = objectId(conceptId)
results = GolrSearchQuery(term=conceptId,
fq={
'id': conceptId
},
rows=1,
hl=False).exec()
entries = []
for d in results['docs']:
c = parse_concept(d)
details = {}
details['iri'] = get_concept_property(d, 'iri')
details['taxon'] = get_concept_property(d, 'taxon')
details['taxon_label'] = get_concept_property(d, 'taxon_label')
details['taxon_label_synonym'] = get_concept_property(
d, 'taxon_label_synonym')
if details['taxon_label_synonym'] is not None:
details['taxon_label_synonym'] = ', '.join(
details['taxon_label_synonym'])
c['details'] = [{
'tag': k,
'value': v
} for k, v in details.items() if v is not None]
entries += [c]
return jsonify(entries)
def test_cursor():
"""
Tests rows and start parameters.
First fetch 100 docs, then same query but iterate with cursor in increments of ten.
The two sets of IDs returned should be identicial
"""
q = GolrSearchQuery("abnormal", rows=100)
results = q.exec()
docs = results['docs']
ids = set([d['id'] for d in docs])
print('Init ids={}'.format(ids))
assert len(ids) == 100
matches = set()
for i in range(0,10):
q = GolrSearchQuery("abnormal", start=i*10, rows=10)
docs = q.exec()['docs']
next_ids = [d['id'] for d in docs]
assert len(next_ids) == 10
print('Next ids (from {}) = {}'.format(i*10, next_ids))
matches.update(next_ids)
assert len(matches) == 100
assert len(matches.intersection(ids)) == 100
def main():
"""
Wrapper for OGR
"""
parser = argparse.ArgumentParser(
description='Command line interface to python-ontobio.golr library'
"""
Provides command line interface onto the ontobio.golr python library, a high level
abstraction layer over Monarch and GO solr indices.
""",
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-A',
'--associations',
dest='associations',
action='store_true',
default=False,
help='Path to output file')
parser.add_argument('-s',
'--settings',
type=str,
help='Path to config file')
parser.add_argument('-o',
'--outfile',
type=str,
required=False,
help='Path to output file')
parser.add_argument('-f',
'--facets',
type=str,
required=False,
help='Facet fields: comma-delimited')
parser.add_argument('-q',
'--fq',
type=json.loads,
default={},
required=False,
help='Facet query (solr fq) - should be json')
parser.add_argument(
'-Q',
'--qargs',
type=json.loads,
default={},
required=False,
help='Query to be passed directly to python golr_associations query')
parser.add_argument('-l',
'--legacy_solr',
dest='legacy_solr',
action='store_true',
default=False,
help='Set for legacy solr schema (solr3 golr)')
parser.add_argument('-u',
'--url',
type=str,
required=False,
help='Solr URL. E.g. http://localhost:8983/solr/golr')
parser.add_argument('-v',
'--verbosity',
default=0,
action='count',
help='Increase output verbosity')
parser.add_argument('search', type=str, help='Search terms')
args = parser.parse_args()
if args.verbosity >= 2:
logging.basicConfig(level=logging.DEBUG)
elif args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.WARNING)
logging.info("Welcome!")
facets = []
if args.facets is not None:
facets = args.facets.split(",")
config = None
if args.settings is not None:
from ontobio.config import load_config
config = load_config(args.settings)
results = None
if args.associations:
q = None
if args.search != '%':
q = args.search
q = GolrAssociationQuery(q=q,
is_go=args.legacy_solr,
fq=args.fq,
facet_fields=facets,
url=args.url)
results = q.exec()
#print("RESULTS={}".format(results))
docs = results['associations']
print("RESULTS: {}".format(len(docs)))
for r in docs:
print(str(r))
else:
logging.info("FQ={}".format(args.fq))
q = GolrSearchQuery(args.search,
is_go=args.legacy_solr,
fq=args.fq,
facet_fields=facets,
url=args.url)
results = q.exec()
#print("RESULTS={}".format(results))
docs = results['docs']
print("RESULTS: {}".format(len(docs)))
for r in docs:
print(" {} '{}' {} // {}".format(r['id'], r['label'], r['score'],
r['category']))
if len(facets) > 0:
#from collections import OrderedDict
fcs = results['facet_counts']
for f in facets:
d = fcs[f]
print(str(d))
print("## FACET: {}".format(f))
for k, v in sorted(d.items(), key=lambda t: -t[1]):
print(" {:5d}: {}".format(v, k))
def test_solr_404():
q = GolrSearchQuery("abnormal")
q.update_solr_url("https://httpbin.org/status/404")
pytest.raises(pysolr.SolrError, q.search)
class TestGolrSearchQuery():
@classmethod
def setup_class(self):
self.manager = GolrSearchQuery()
# Mock the PySolr search function to
# return our test docs
input_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/solr-docs.json')
input_docs = json.load(open(input_fh))
self.test_results = pysolr.Results(input_docs)
self.manager.solr.search = MagicMock(return_value=self.test_results)
@classmethod
def teardown_class(self):
self.manager = None
def test_longest_hl(self):
test_data = [
"<em>Muscle</em> <em>atrophy</em>, generalized",
"Generalized <em>muscle</em> degeneration",
"Diffuse skeletal <em>muscle</em> wasting"
]
expected = "<em>Muscle</em> <em>atrophy</em>, generalized"
results = self.manager._get_longest_hl(test_data)
assert expected == results
def test_longest_hl_ambiguous(self):
test_data = [
"<em>Muscle</em> <em>atrophy</em>, generalized",
"Generalized <em>muscle</em> degeneration",
"Diffuse skeletal <em>muscle</em> wasting",
"<em>Muscle</em> <em>atrophy</em>, not generalized",
]
expected = "<em>Muscle</em> <em>atrophy</em>, generalized"
results = self.manager._get_longest_hl(test_data)
assert expected == results
def test_hl_to_string(self):
test_data = "Foo <em>Muscle</em> bar <em>atrophy</em>, generalized"
expected = "Foo Muscle bar atrophy, generalized"
results = self.manager._hl_as_string(test_data)
assert expected == results
def test_invalid_xml(self):
test_data = "Foo<Foo> <em>Muscle</em> bar <em>atrophy</em>, generalized"
pytest.raises(ET.ParseError, self.manager._hl_as_string, test_data)
def test_autocomplete_doc_conversion(self):
"""
Given a sample solr output as a pysolr.Results object
test that _process_autocomplete_results returns the
expected object
"""
expected_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/autocomplete-expected.json')
processed_docs = json.load(open(expected_fh))
output_docs = self.manager._process_autocomplete_results(self.test_results)
assert json.dumps(processed_docs, sort_keys=True) == \
json.dumps(output_docs,
default=lambda obj: getattr(obj, '__dict__', str(obj)),
sort_keys=True)
def test_search_doc_conversion(self):
"""
Given a sample solr output as a pysolr.Results object
test that _process_autocomplete_results returns the
expected object
"""
expected_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/search-expected.json')
processed_docs = json.load(open(expected_fh))
output_docs = self.manager._process_search_results(self.test_results)
assert json.dumps(processed_docs, sort_keys=True) == \
json.dumps(output_docs,
default=lambda obj: getattr(obj, '__dict__', str(obj)),
sort_keys=True)
def test_search(self):
"""
Given a mock PySolr.search method test that
search() returns the expected object
"""
expected_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/search-expected.json')
processed_docs = json.load(open(expected_fh))
output_docs = self.manager.search()
assert json.dumps(processed_docs, sort_keys=True) == \
json.dumps(output_docs,
default=lambda obj: getattr(obj, '__dict__', str(obj)),
sort_keys=True)
def test_autocomplete(self):
"""
Given a mock PySolr.search method test that
autocomplete() returns the expected object
"""
expected_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/autocomplete-expected.json')
processed_docs = json.load(open(expected_fh))
output_docs = self.manager.autocomplete()
assert json.dumps(processed_docs, sort_keys=True) == \
json.dumps(output_docs,
default=lambda obj: getattr(obj, '__dict__', str(obj)),
sort_keys=True)
def test_autocomplete_no_category(self):
"""
Test for document without a category
"""
# Provide a new mock file
input_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/autocomplete-nocat.json')
input_docs = json.load(open(input_fh))
self.test_results = pysolr.Results(input_docs)
self.manager.solr.search = MagicMock(return_value=self.test_results)
expected_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/autocomplete-nocat-expect.json')
processed_docs = json.load(open(expected_fh))
output_docs = self.manager.autocomplete()
print(json.dumps(output_docs,
default=lambda obj: getattr(obj, '__dict__', str(obj)),
sort_keys=True))
assert json.dumps(processed_docs, sort_keys=True) == \
json.dumps(output_docs,
default=lambda obj: getattr(obj, '__dict__', str(obj)),
sort_keys=True)
def search(term, args):
q = GolrSearchQuery(term, args)
return q.search()