def test_search_bool_term():
concepts = []
bool_term = {}
bool_term[TERM_FIELD] = TERM_VALUE
search_concept = wh.SearchableConcept(cui=CUI, ontology=ONTOLOGY, rank='10',
semanticType=SEMTYPE)
concepts.append(search_concept)
date_range = wh.Range(begin=RANGE_BEGIN, end=RANGE_END)
range_map = {}
range_map[RANGE_FIELD] = date_range
query = wh.Query(concepts=concepts, date_range=range_map, boolTerm=bool_term)
documents = wh.Documents("10", "0")
returns = wh.ReturnsModel(documents)
response = IML_TEST.search(corpus=CORPUS, query=query, returns=returns)
search_model = wh.SearchModel._from_dict(response.get_result())
result_documents = search_model.documents
for ranked_doc in result_documents:
assert ranked_doc.document_id is not None
assert ranked_doc.metadata is not None
for key in ranked_doc.metadata:
assert key is not None
assert ranked_doc.metadata[key] is not None
assert ranked_doc.corpus == CORPUS
assert ranked_doc.links is not None
doc_links = ranked_doc.links
assert doc_links.href_search_matches is not None
assert doc_links.href_categories is not None
def test_search_keyword():
phrase = 'COPD AND (smoker OR smoking)'
operands = []
copd_operand = {}
copd_operand['ontology'] = 'text'
copd_operand['operandName'] = 'COPD'
copd_operand['text'] = 'COPD'
operands.append(copd_operand)
smoker_operand = {}
smoker_operand['ontology'] = 'text'
smoker_operand['operandName'] = 'smoker'
smoker_operand['text'] = 'smoker'
operands.append(smoker_operand)
smoking_operand = {}
smoking_operand['ontology'] = 'text'
smoking_operand['operandName'] = 'smoking'
smoking_operand['text'] = 'smoking'
operands.append(smoking_operand)
query = wh.Query(boolExpression=phrase, concepts=operands)
documents = wh.Documents("10", "0")
returns = wh.ReturnsModel(documents)
response = IML_TEST.search(corpus=CORPUS, query=query, returns=returns)
search_model = wh.SearchModel._from_dict(response.get_result())
result_documents = search_model.documents
for ranked_doc in result_documents:
assert ranked_doc.document_id is not None
assert ranked_doc.metadata is not None
for key in ranked_doc.metadata:
assert key is not None
assert ranked_doc.metadata[key] is not None
assert ranked_doc.corpus == CORPUS
assert ranked_doc.links is not None
doc_links = ranked_doc.links
assert doc_links.href_search_matches is not None
assert doc_links.href_categories is not None
def test_search_multiple_concepts():
concepts = []
search_concept1 = wh.SearchableConcept(cui=CUI, ontology=ONTOLOGY, rank='10',
semanticType=SEMTYPE)
concepts.append(search_concept1)
search_concept2 = wh.SearchableConcept(cui=SECOND_CUI, ontology=ONTOLOGY, rank='10',
semanticType=SECOND_SEMTYPE)
concepts.append(search_concept2)
query = wh.Query(concepts=concepts)
documents = wh.Documents("10", "0")
returns = wh.ReturnsModel(documents)
response = IML_TEST.search(corpus=CORPUS, query=query, returns=returns)
search_model = wh.SearchModel._from_dict(response.get_result())
result_documents = search_model.documents
for ranked_doc in result_documents:
assert ranked_doc.document_id is not None
assert ranked_doc.metadata is not None
for key in ranked_doc.metadata:
assert key is not None
assert ranked_doc.metadata[key] is not None
assert ranked_doc.corpus == CORPUS
assert ranked_doc.links is not None
doc_links = ranked_doc.links
assert doc_links.href_search_matches is not None
assert doc_links.href_categories is not None
def test_search_returns_attributes():
attributes = wh.Attributes()
returns = wh.ReturnsModel(None, None, None, attributes)
response = IML_TEST.search(CORPUS, returns, query=None)
search_model = wh.SearchModel._from_dict(response.get_result())
result_attributes = search_model.attributes
for attribute in result_attributes:
assert attribute.attribute_id is not None
assert attribute.count > 0
def test_search_returns_typeahead():
type_list = []
type_list.append(SEMTYPE)
typeahead = wh.Typeahead(ONTOLOGY, "hear", type_list, 5, True)
returns = wh.ReturnsModel(typeahead=typeahead)
response = IML_TEST.search(CORPUS, returns, query=None)
search_model = wh.SearchModel._from_dict(response.get_result())
result_typehead = search_model.typeahead
for concept in result_typehead:
assert concept.cui is not None
def test_search_returns_passages():
concepts = []
search_concept = wh.SearchableConcept(cui=CUI, ontology=ONTOLOGY, rank='10',
semanticType=SEMTYPE)
concepts.append(search_concept)
query = wh.Query(concepts=concepts)
documents = wh.Documents("10", "0")
matches = [search_concept]
passages = wh.Passages(concepts_to_highlight=matches, limit=3, search_tag_begin='<search_span>',
search_tag_end='</search_span>', related_tag_begin='<related_span>',
related_tag_end='</related_tag_end>', min_score='0.1')
returns = wh.ReturnsModel(documents, passages=passages)
def test_search_returns_concepts():
title = wh.Title(0)
concepts = []
search_concept = wh.SearchableConcept(cui=CUI, ontology=ONTOLOGY, rank='10',
semanticType=SEMTYPE)
concepts.append(search_concept)
query = wh.Query(title=title, concepts=concepts)
cooccurring_concepts = wh.Concepts(ONTOLOGY, 20)
returns = wh.ReturnsModel(None, cooccurring_concepts)
response = IML_TEST.search(corpus=CORPUS, query=query, returns=returns)
search_model = wh.SearchModel._from_dict(response.get_result())
result_concepts = search_model.concepts
for concept in result_concepts:
assert concept.cui is not None
def test_search_sorted_results():
concepts = []
search_concept = wh.SearchableConcept(cui=CUI, ontology=ONTOLOGY, rank='10',
semanticType=SEMTYPE)
concepts.append(search_concept)
query = wh.Query(concepts=concepts)
metadata = []
metadata.append("abstract")
metadata.append(SORT_FIELD)
sort_entries = []
order = wh.Order('ASC')
sort = wh.SortEntry(SORT_FIELD, order)
sort_entries.append(sort)
documents = wh.Documents("10", "0", metadata, None, sort=sort_entries)
returns = wh.ReturnsModel(documents)
def test_returns_aggregations():
agg_map = {}
aggregations = wh.Aggregations(limit=VALID_LIMIT)
authors = {}
authors['limit'] = 20
agg_map['authors'] = aggregations
returns = wh.ReturnsModel(aggregations=agg_map)
response = IML_TEST.search(CORPUS, returns, query=None)
search_model = wh.SearchModel._from_dict(response.get_result())
results_aggregations = search_model.aggregations
for key in results_aggregations:
aggregations = results_aggregations[key]
for aggregation in aggregations:
agg = wh.AggregationModel._from_dict(aggregation)
assert agg.name is not None
assert agg.document_count > 0
def test_search_bool_regexp():
bool_regexp = {}
bool_regexp['title'] = BOOLEAN_REGEX
query = wh.Query(boolRegexp=bool_regexp)
documents = wh.Documents("10", "0")
returns = wh.ReturnsModel(documents)
response = IML_TEST.search(corpus=CORPUS, query=query, returns=returns)
search_model = wh.SearchModel._from_dict(response.get_result())
result_documents = search_model.documents
for ranked_doc in result_documents:
assert ranked_doc.document_id is not None
assert ranked_doc.metadata is not None
for key in ranked_doc.metadata:
assert key is not None
assert ranked_doc.metadata[key] is not None
assert ranked_doc.corpus == CORPUS
assert ranked_doc.links is not None
doc_links = ranked_doc.links
assert doc_links.href_search_matches is not None
assert doc_links.href_categories is not None
def test_search_boolean_phrase():
concepts = []
phrase = BOOL_PHRASE
query = wh.Query(boolExpression=phrase, concepts=concepts)
documents = wh.Documents("10", "0")
returns = wh.ReturnsModel(documents)
response = IML_TEST.search(corpus=CORPUS, query=query, returns=returns)
search_model = wh.SearchModel._from_dict(response.get_result())
result_documents = search_model.documents
for ranked_doc in result_documents:
assert ranked_doc.document_id is not None
assert ranked_doc.metadata is not None
for key in ranked_doc.metadata:
assert key is not None
assert ranked_doc.metadata[key] is not None
assert ranked_doc.corpus == CORPUS
assert ranked_doc.links is not None
doc_links = ranked_doc.links
assert doc_links.href_search_matches is not None
assert doc_links.href_categories is not None
def test_search_regexp():
regexps = []
regexp = {}
regexp[REGEX_FIELD] = REGEX
regexps.append(regexp)
query = wh.Query(regexp=regexps)
documents = wh.Documents("10", "0")
returns = wh.ReturnsModel(documents)
response = IML_TEST.search(corpus=CORPUS, query=query, returns=returns)
search_model = wh.SearchModel._from_dict(response.get_result())
result_documents = search_model.documents
for ranked_doc in result_documents:
assert ranked_doc.document_id is not None
assert ranked_doc.metadata is not None
for key in ranked_doc.metadata:
assert key is not None
assert ranked_doc.metadata[key] is not None
assert ranked_doc.corpus == CORPUS
assert ranked_doc.links is not None
doc_links = ranked_doc.links
assert doc_links.href_search_matches is not None
assert doc_links.href_categories is not None
def test_returns_date_histogram():
concepts = []
search_concept = wh.SearchableConcept(cui=CUI, ontology=ONTOLOGY, rank='10',
semanticType=SEMTYPE)
concepts.append(search_concept)
query = wh.Query(concepts=concepts)
date_histogram = wh.DateHistograms(interval='1y')
metadata = []
metadata.append("abstract")
metadata.append(RANGE_FIELD)
histogram_map = {}
histogram_map[RANGE_FIELD] = date_histogram
documents = wh.Documents(limit="10", offset="0", metadata=metadata)
returns = wh.ReturnsModel(documents, None, None, None, None, None, None, None, histogram_map)
response = IML_TEST.search(corpus=CORPUS, query=query, returns=returns)
search_model = wh.SearchModel._from_dict(response.get_result())
result_documents = search_model.documents
for ranked_doc in result_documents:
assert ranked_doc.document_id is not None
assert ranked_doc.metadata is not None
for key in ranked_doc.metadata:
assert key is not None
assert ranked_doc.metadata[key] is not None
assert ranked_doc.corpus == CORPUS
assert ranked_doc.links is not None
doc_links = ranked_doc.links
assert doc_links.href_search_matches is not None
assert doc_links.href_categories is not None
result_histograms = search_model.date_histograms
for histogram_key in result_histograms:
years_and_hits = result_histograms[histogram_key]
for year in years_and_hits:
year_date = wh.YearAndHits()
year_and_hits = year_date._from_dict(year)
assert year_and_hits.date is not None
assert year_and_hits.hits > -1
def test_search_no_corpus():
try:
returns = wh.ReturnsModel()
IML_TEST.search(None, returns)
except ValueError as exp:
assert exp is not None
