def test_searcher_returns_dictionary(searcher: Searcher, mocker):
"""
The searcher must return a json formatted SRA resultset
"""
mocker.patch("Bio.Entrez.esearch")
Entrez.esearch.return_value = io.StringIO("{}")
result = searcher.search("Human", max_results=3)
assert isinstance(result, dict)
def test_searcher_searches_sra(searcher: Searcher, mocker):
"""
Tests if the searcher, when supplied with a valid search string,
calls the correct Biopython's Entrez methods
"""
# We need to supply a return value to the esearch function.
# That return value must be a buffer.
mocker.patch("Bio.Entrez.esearch")
Entrez.esearch.return_value = io.StringIO("{}")
searcher.search('"H**o sapiens"[Organism]')
# pylint: disable=no-member
Entrez.esearch.assert_called_with(
"sra", '"H**o sapiens"[Organism]', retmax=10, retmode="json"
)
def test_searcher_configurer_entrez():
"""
In order for everything to work, the Searcher must set Entrez's e-mail and
API Key parameters
"""
Searcher(email="*****@*****.**", api_key="3141516")
assert Entrez.email == "*****@*****.**"
assert Entrez.api_key == "3141516"
def test_searcher_initialization(searcher):
"""
Tests a searcher initialization parameters
"""
assert isinstance(searcher, Searcher)
assert searcher.db == "sra"
new_searcher = Searcher("*****@*****.**", db="other_db")
assert new_searcher.db == "other_db"
def test_searcher_format(searcher: Searcher):
"""
The searcher must return data in an specified format
"""
result = searcher.search("Human", max_results=3)
assert isinstance(result, dict)
assert "header" in result.keys()
assert "esearchresult" in result.keys()
jsonschema.validate(result, SEARCH_RESULT_SCHEMA)
def test_fetch_result(searcher: Searcher, mocker):
"""
Given an Entrez UID, the searcher must acquire the related data
"""
mocker.patch("Bio.Entrez.efetch")
Entrez.efetch.return_value = open(
Path(__file__).parent.absolute().joinpath("sample_efetch_result.xml")
)
data = searcher.fetch("8801091")
# pylint: disable=no-member
Entrez.efetch.assert_called()
assert data
assert isinstance(data, dict)
def searcher():
"""
Fixture that provides a Searcher instance
"""
return Searcher("*****@*****.**")