def get(self, term):
"""
Returns list of matching concepts or entities using lexical search
"""
input_args = layperson_parser.parse_args()
# params that don't directly translate to solr controller
filtered_params = [
'phenotype_group', 'phenotype_group_label', 'anatomical_system',
'anatomical_system_label'
]
args = {
k: v
for k, v in input_args.items() if k not in filtered_params
}
args['fq'] = {}
if input_args['phenotype_group'] is not None:
args['fq']['phenotype_closure'] = input_args['phenotype_group']
if input_args['phenotype_group_label'] is not None:
args['fq']['phenotype_closure_label'] = input_args[
'phenotype_group_label']
if input_args['anatomical_system'] is not None:
args['fq']['anatomy_closure'] = input_args['anatomical_system']
if input_args['anatomical_system_label'] is not None:
args['fq']['anatomy_closure_label'] = input_args[
'anatomical_system_label']
q = GolrLayPersonSearch(term, user_agent=USER_AGENT, **args)
results = q.autocomplete()
return results
def setup_class(self):
self.manager = GolrLayPersonSearch()
# Mock the PySolr search function to
# return our test docs
input_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/layperson-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)
class TestGolrSearchParams():
@classmethod
def setup_class(self):
self.manager = GolrLayPersonSearch()
@classmethod
def teardown_class(self):
self.manager = None
def test_prefix_filters(self):
"""
Test that prefix filters are converted
properly to solr params
"""
prefix_filter = [
'-OMIA',
'-Orphanet',
'DO',
'OMIM',
'MONDO'
]
expected = [
'-prefix:"OMIA"',
'-prefix:"Orphanet"',
'prefix:"DO" OR prefix:"OMIM" OR prefix:"MONDO"'
]
self.manager.prefix = prefix_filter
params = self.manager.solr_params()
assert params['fq'] == expected
class TestGolrLayPersonSearch():
@classmethod
def setup_class(self):
self.manager = GolrLayPersonSearch()
# Mock the PySolr search function to
# return our test docs
input_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/input/layperson-docs.json')
input_docs = json.load(open(input_fh))
self.pysolr_results = pysolr.Results(input_docs)
self.manager.solr.search = MagicMock(return_value=self.pysolr_results)
@classmethod
def teardown_class(self):
self.manager = None
def test_lay_doc_conversion(self):
"""
Given a sample solr output as a pysolr.Results object
test that _process_layperson_results returns the
expected object
"""
expected_fh = os.path.join(os.path.dirname(__file__),
'resources/solr/expected/layperson.json')
processed_docs = json.load(open(expected_fh))
output_docs = self.manager._process_layperson_results(
self.pysolr_results)
assert json.dumps(processed_docs,
sort_keys=True) == json.dumps(output_docs,
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/expected/layperson.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,
sort_keys=True)
class TestGolrSearchParams():
@classmethod
def setup_class(self):
self.manager = GolrLayPersonSearch()
@classmethod
def teardown_class(self):
self.manager = None
def test_prefix_filters(self):
"""
Test that prefix filters are converted
properly to solr params
"""
prefix_filter = ['-OMIA', '-Orphanet', 'DO', 'OMIM', 'MONDO']
expected = [
'-prefix:("OMIA" OR "Orphanet")',
'prefix:("DO" OR "OMIM" OR "MONDO")'
]
self.manager.prefix = prefix_filter
params = self.manager.solr_params()
assert params['fq'] == expected
def test_prefix_filters_include_eq(self):
"""
Test that prefix filters are converted
properly to solr params
"""
prefix_filter = ['-OMIA', '-Orphanet', 'DO', 'OMIM', 'MONDO']
expected = [
'(-prefix:"OMIA" OR -equivalent_curie:OMIA\:*)',
'(-prefix:"Orphanet" OR -equivalent_curie:Orphanet\:*)',
'((prefix:"DO" OR equivalent_curie:DO\:*) OR (prefix:"OMIM" OR '
'equivalent_curie:OMIM\:*) OR (prefix:"MONDO" OR equivalent_curie:MONDO\:*))'
]
self.manager.prefix = prefix_filter
self.manager.include_eqs = True
params = self.manager.solr_params()
assert params['fq'] == expected
def setup_class(self):
self.manager = GolrLayPersonSearch()
