async def test_correct_data_is_set_to_json_when_replacing(self):
"""Test operator replaces object and adds necessary info."""
operator = Operator(self.client)
with patch(
"metadata_backend.api.operators.Operator._replace_object_from_db", return_value=self.accession_id
) as mocked_insert:
with patch("metadata_backend.api.operators.datetime") as m_date:
m_date.utcnow.return_value = datetime.datetime(2020, 4, 14)
acc = await (operator._format_data_to_replace_and_add_to_db("study", self.accession_id, {}))
mocked_insert.assert_called_once_with(
"study",
self.accession_id,
{"accessionId": self.accession_id, "dateModified": datetime.datetime(2020, 4, 14)},
)
self.assertEqual(acc, self.accession_id)
async def test_query_skip_and_limit_are_set_correctly(self):
"""Test custom skip and limits."""
operator = Operator(self.client)
data = {"foo": "bar"}
result = []
operator.db_service.do_aggregate.side_effect = [result, [{"total": 0}]]
with patch(
"metadata_backend.api.operators.Operator._format_read_data",
return_value=data,
):
await operator.query_metadata_database("sample", {}, 3, 50, [])
calls = [
call(
"sample",
[
{"$match": {}},
{"$redact": {"$cond": {"if": {}, "then": "$$DESCEND", "else": "$$PRUNE"}}},
{"$skip": 50 * (3 - 1)},
{"$limit": 50},
{"$project": {"_id": 0}},
],
),
call(
"sample",
[
{"$match": {}},
{"$redact": {"$cond": {"if": {}, "then": "$$DESCEND", "else": "$$PRUNE"}}},
{"$count": "total"},
],
),
]
operator.db_service.do_aggregate.assert_has_calls(calls, any_order=True)
self.assertEqual(operator.db_service.do_aggregate.call_count, 2)
async def test_query_result_is_parsed_correctly(self):
"""Test JSON is read and correct pagination values are returned."""
operator = Operator(self.client)
multiple_result = [
{
"dateCreated": datetime.datetime(2020, 6, 14, 0, 0),
"dateModified": datetime.datetime(2020, 6, 14, 0, 0),
"accessionId": "EGA123456",
"foo": "bar",
},
{
"dateCreated": datetime.datetime(2020, 6, 14, 0, 0),
"dateModified": datetime.datetime(2020, 6, 14, 0, 0),
"accessionId": "EGA123456",
"foo": "bar",
},
]
study_total = [{"total": 100}]
operator.db_service.do_aggregate.side_effect = [multiple_result, study_total]
query = MultiDictProxy(MultiDict([]))
(
parsed,
page_num,
page_size,
total_objects,
) = await operator.query_metadata_database("sample", query, 1, 10, [])
for doc in parsed:
self.assertEqual(doc["dateCreated"], "2020-06-14T00:00:00")
self.assertEqual(doc["dateModified"], "2020-06-14T00:00:00")
self.assertEqual(doc["accessionId"], "EGA123456")
self.assertEqual(page_num, 1)
self.assertEqual(page_size, 2)
self.assertEqual(total_objects, 100)
async def test_json_update_raises_if_not_exists(self):
"""Test update method raises error."""
operator = Operator(self.client)
operator.db_service.exists.return_value = False
operator.db_service.replace.return_value = True
with self.assertRaises(HTTPNotFound):
await operator.update_metadata_object("study", self.accession_id, {})
operator.db_service.update.assert_called_once()
async def test_deleting_metadata_deletes_json_and_xml(self):
"""Test metadata is deleted."""
operator = Operator(self.client)
operator.db_service.db_client = self.client
operator.db_service.exists.return_value = True
operator.db_service.delete.return_value = True
await operator.delete_metadata_object("sample", "EGA123456")
self.assertEqual(operator.db_service.delete.call_count, 2)
operator.db_service.delete.assert_called_with("sample", "EGA123456")
async def test_deleting_metadata_delete_raises_bad_request(self):
"""Test bad request error raised with delete."""
operator = Operator(self.client)
operator.db_service.db_client = self.client
operator.db_service.exists.return_value = True
operator.db_service.delete.return_value = False
with self.assertRaises(HTTPBadRequest):
await operator.delete_metadata_object("sample", "EGA123456")
self.assertEqual(operator.db_service.delete.call_count, 2)
operator.db_service.delete.assert_called_with("sample", "EGA123456")
async def test_wront_data_is_set_to_json_when_replacing(self):
"""Test operator replace catches error."""
operator = Operator(self.client)
with patch("metadata_backend.api.operators.Operator._replace_object_from_db", return_value=self.accession_id):
with patch("metadata_backend.api.operators.datetime") as m_date:
m_date.utcnow.return_value = datetime.datetime(2020, 4, 14)
with self.assertRaises(HTTPBadRequest):
await (
operator._format_data_to_replace_and_add_to_db(
"study",
self.accession_id,
{
"accessionId": self.accession_id,
"dateCreated": datetime.datetime(2020, 4, 14),
"dateModified": datetime.datetime(2020, 4, 14),
"publishDate": datetime.datetime(2020, 6, 14),
},
)
)
async def test_non_empty_query_result_raises_notfound(self):
"""Test that 404 is raised with empty query result."""
operator = Operator(self.client)
operator.db_service.query = MagicMock()
query = MultiDictProxy(MultiDict([]))
with patch(
"metadata_backend.api.operators.Operator._format_read_data",
return_value=[],
):
with self.assertRaises(HTTPNotFound):
await operator.query_metadata_database("study", query, 1, 10, [])
async def test_json_create_passes_and_returns_accessionId(self):
"""Test create method for JSON works."""
operator = Operator(self.client)
data = {
"centerName": "GEO",
"alias": "GSE10966",
"descriptor": {"studyTitle": "Highly", "studyType": "Other"},
}
operator.db_service.create.return_value = True
accession = await operator.create_metadata_object("study", data)
operator.db_service.create.assert_called_once()
self.assertEqual(accession, self.accession_id)
async def test_working_query_params_are_passed_to_db_query(self):
"""Test that database is called with correct query."""
operator = Operator(self.client)
study_test = [
{
"publishDate": datetime.datetime(2020, 6, 14, 0, 0),
"accessionId": "EDAG3945644754983408",
"dateCreated": datetime.datetime(2020, 6, 14, 0, 0),
"dateModified": datetime.datetime(2020, 6, 14, 0, 0),
}
]
study_total = [{"total": 0}]
operator.db_service.do_aggregate.side_effect = [study_test, study_total]
query = MultiDictProxy(MultiDict([("studyAttributes", "foo")]))
await operator.query_metadata_database("study", query, 1, 10, [])
calls = [
call(
"study",
[
{
"$match": {
"$or": [
{"studyAttributes.tag": re.compile(".*foo.*", re.IGNORECASE)},
{"studyAttributes.value": re.compile(".*foo.*", re.IGNORECASE)},
]
}
},
{"$redact": {"$cond": {"if": {}, "then": "$$DESCEND", "else": "$$PRUNE"}}},
{"$skip": 0},
{"$limit": 10},
{"$project": {"_id": 0}},
],
),
call(
"study",
[
{
"$match": {
"$or": [
{"studyAttributes.tag": re.compile(".*foo.*", re.IGNORECASE)},
{"studyAttributes.value": re.compile(".*foo.*", re.IGNORECASE)},
]
}
},
{"$redact": {"$cond": {"if": {}, "then": "$$DESCEND", "else": "$$PRUNE"}}},
{"$count": "total"},
],
),
]
operator.db_service.do_aggregate.assert_has_calls(calls, any_order=True)
def test_operator_fixes_single_document_presentation(self):
"""Test datetime is fixed and id removed."""
study_test = {
"publishDate": datetime.datetime(2020, 6, 14, 0, 0),
"accessionId": "EDAG3945644754983408",
"dateCreated": datetime.datetime(2020, 6, 14, 0, 0),
"dateModified": datetime.datetime(2020, 6, 14, 0, 0),
}
result = Operator(self.client)._format_single_dict("study", study_test)
self.assertEqual(result["publishDate"], "2020-06-14T00:00:00")
self.assertEqual(result["dateCreated"], "2020-06-14T00:00:00")
self.assertEqual(result["dateModified"], "2020-06-14T00:00:00")
with self.assertRaises(KeyError):
result["_Id"]
async def test_non_working_query_params_are_not_passed_to_db_query(self):
"""Test that database with empty query, when url params are wrong."""
operator = Operator(self.client)
study_test = [
{
"publishDate": datetime.datetime(2020, 6, 14, 0, 0),
"accessionId": "EDAG3945644754983408",
"dateCreated": datetime.datetime(2020, 6, 14, 0, 0),
"dateModified": datetime.datetime(2020, 6, 14, 0, 0),
}
]
study_total = [{"total": 0}]
operator.db_service.do_aggregate.side_effect = [study_test, study_total]
query = MultiDictProxy(MultiDict([("swag", "littinen")]))
with patch(
"metadata_backend.api.operators.Operator._format_read_data",
return_value=study_test,
):
await operator.query_metadata_database("study", query, 1, 10, [])
calls = [
call(
"study",
[
{"$match": {}},
{"$redact": {"$cond": {"if": {}, "then": "$$DESCEND", "else": "$$PRUNE"}}},
{"$skip": 0},
{"$limit": 10},
{"$project": {"_id": 0}},
],
),
call(
"study",
[
{"$match": {}},
{"$redact": {"$cond": {"if": {}, "then": "$$DESCEND", "else": "$$PRUNE"}}},
{"$count": "total"},
],
),
]
operator.db_service.do_aggregate.assert_has_calls(calls, any_order=True)
self.assertEqual(operator.db_service.do_aggregate.call_count, 2)
async def test_reading_metadata_works(self):
"""Test JSON is read from db correctly."""
operator = Operator(self.client)
data = {
"dateCreated": datetime.datetime(2020, 6, 14, 0, 0),
"dateModified": datetime.datetime(2020, 6, 14, 0, 0),
"accessionId": "EGA123456",
"foo": "bar",
}
operator.db_service.read.return_value = data
read_data, c_type = await operator.read_metadata_object("sample", "EGA123456")
operator.db_service.read.assert_called_once_with("sample", "EGA123456")
self.assertEqual(c_type, "application/json")
self.assertEqual(
read_data,
{
"dateCreated": "2020-06-14T00:00:00",
"dateModified": "2020-06-14T00:00:00",
"accessionId": "EGA123456",
"foo": "bar",
},
)
async def test_db_error_update_raises_400_error(self):
"""Test update metadata HTTPBadRequest is raised."""
operator = Operator(self.client)
operator.db_service.exists.side_effect = ConnectionFailure
with self.assertRaises(HTTPBadRequest):
await operator.update_metadata_object("study", self.accession_id, {})
async def test_db_error_raises_400_error(self):
"""Test read metadata HTTPBadRequest is raised."""
operator = Operator(self.client)
operator.db_service.read.side_effect = ConnectionFailure
with self.assertRaises(HTTPBadRequest):
await operator.read_metadata_object("study", "EGA123456")
async def test_reading_with_non_valid_id_raises_error(self):
"""Test read metadata HTTPNotFound is raised."""
operator = Operator(self.client)
operator.db_service.read.return_value = False
with self.assertRaises(HTTPNotFound):
await operator.read_metadata_object("study", "EGA123456")