import json import os from datetime import datetime import numpy as np import numpy.testing as nptu import pytest from pymongo.errors import ConfigurationError from maggma.core import StoreError from maggma.stores import GridFSStore, MongoStore from maggma.stores.gridfs import GridFSURIStore, files_collection_fields @pytest.fixture() def mongostore(): store = MongoStore("maggma_test", "test") store.connect() yield store store._collection.drop() @pytest.fixture() def gridfsstore(): store = GridFSStore("maggma_test", "test", key="task_id") store.connect() yield store store._files_collection.drop() store._chunks_collection.drop() def test_update(gridfsstore): data1 = np.random.rand(256) data2 = np.random.rand(256) tic = datetime(2018, 4, 12, 16) # Test metadata storage gridfsstore.update([{"task_id": "mp-1", "data": data1, gridfsstore.last_updated_field: tic}]) assert gridfsstore._files_collection.find_one({"metadata.task_id": "mp-1"}) is not None # Test storing data gridfsstore.update([{"task_id": "mp-1", "data": data2, gridfsstore.last_updated_field: tic}]) assert len(list(gridfsstore.query({"task_id": "mp-1"}))) == 1 assert "task_id" in gridfsstore.query_one({"task_id": "mp-1"}) nptu.assert_almost_equal(gridfsstore.query_one({"task_id": "mp-1"})["data"], data2, 7) # Test storing compressed data gridfsstore = GridFSStore("maggma_test", "test", key="task_id", compression=True) gridfsstore.connect() gridfsstore.update([{"task_id": "mp-1", "data": data1}]) assert gridfsstore._files_collection.find_one({"metadata.compression": "zlib"}) is not None nptu.assert_almost_equal(gridfsstore.query_one({"task_id": "mp-1"})["data"], data1, 7) def test_remove(gridfsstore): data1 = np.random.rand(256) data2 = np.random.rand(256) tic = datetime(2018, 4, 12, 16) gridfsstore.update([{"task_id": "mp-1", "data": data1, gridfsstore.last_updated_field: tic}]) gridfsstore.update([{"task_id": "mp-2", "data": data2, gridfsstore.last_updated_field: tic}]) assert gridfsstore.query_one(criteria={"task_id": "mp-1"}) assert gridfsstore.query_one(criteria={"task_id": "mp-2"}) gridfsstore.remove_docs({"task_id": "mp-1"}) assert gridfsstore.query_one(criteria={"task_id": "mp-1"}) is None assert gridfsstore.query_one(criteria={"task_id": "mp-2"}) def test_count(gridfsstore): data1 = np.random.rand(256) data2 = np.random.rand(256) tic = datetime(2018, 4, 12, 16) gridfsstore.update([{"task_id": "mp-1", "data": data1, gridfsstore.last_updated_field: tic}]) assert gridfsstore.count() == 1 gridfsstore.update([{"task_id": "mp-2", "data": data2, gridfsstore.last_updated_field: tic}]) assert gridfsstore.count() == 2 assert gridfsstore.count({"task_id": "mp-2"}) == 1 def test_query(gridfsstore): data1 = np.random.rand(256) data2 = np.random.rand(256) tic = datetime(2018, 4, 12, 16) gridfsstore.update([{"task_id": "mp-1", "data": data1, gridfsstore.last_updated_field: tic}]) gridfsstore.update([{"task_id": "mp-2", "data": data2, gridfsstore.last_updated_field: tic}]) doc = gridfsstore.query_one(criteria={"task_id": "mp-1"}) nptu.assert_almost_equal(doc["data"], data1, 7) doc = gridfsstore.query_one(criteria={"task_id": "mp-2"}) nptu.assert_almost_equal(doc["data"], data2, 7) assert gridfsstore.last_updated_field in doc assert gridfsstore.query_one(criteria={"task_id": "mp-3"}) is None def test_query_gridfs_file(gridfsstore): # put the data directly in gridfs, mimicking an existing gridfs collection # generated without the store gridfsstore._collection.put(b"hello world", task_id="mp-1") doc = gridfsstore.query_one() assert doc["data"].decode() == "hello world" assert doc[gridfsstore.key] == "mp-1" def test_last_updated(gridfsstore): data1 = np.random.rand(256) data2 = np.random.rand(256) tic = datetime(2018, 4, 12, 16) gridfsstore.update([{"task_id": "mp-1", "data": data1, gridfsstore.last_updated_field: tic}]) gridfsstore.update([{"task_id": "mp-2", "data": data2, gridfsstore.last_updated_field: tic}]) assert gridfsstore.last_updated == tic toc = datetime(2019, 6, 12, 16) gridfsstore.update([{"task_id": "mp-3", "data": data2, gridfsstore.last_updated_field: toc}]) assert gridfsstore.last_updated == toc tic = datetime(2017, 6, 12, 16) gridfsstore.update([{"task_id": "mp-4", "data": data2, gridfsstore.last_updated_field: tic}]) assert gridfsstore.last_updated == toc def test_groupby(gridfsstore): tic = datetime(2018, 4, 12, 16) for i in range(3): gridfsstore.update( [{"task_id": f"mp-{i}", "a": 1, gridfsstore.last_updated_field: tic}], key=["task_id", "a"], ) for i in range(3, 7): gridfsstore.update( [{"task_id": f"mp-{i}", "a": 2, gridfsstore.last_updated_field: tic}], key=["task_id", "a"], ) groups = list(gridfsstore.groupby("a")) assert len(groups) == 2 assert {g[0]["a"] for g in groups} == {1, 2} by_group = {} for group, docs in groups: by_group[group["a"]] = {d["task_id"] for d in docs} assert by_group[1] == {"mp-0", "mp-1", "mp-2"} assert by_group[2] == {"mp-3", "mp-4", "mp-5", "mp-6"} def test_distinct(gridfsstore): tic = datetime(2018, 4, 12, 16) for i in range(3): gridfsstore.update( [{"task_id": f"mp-{i}", "a": 1, gridfsstore.last_updated_field: tic}], key=["task_id", "a"], ) for i in range(3, 7): gridfsstore.update( [{"task_id": f"mp-{i}", "a": 2, gridfsstore.last_updated_field: tic}], key=["task_id", "a"], ) assert set(gridfsstore.distinct("a")) == {1, 2} def test_eq(mongostore, gridfsstore): assert gridfsstore == gridfsstore assert mongostore != gridfsstore def test_index(gridfsstore): assert gridfsstore.ensure_index("test_key") for field in files_collection_fields: assert gridfsstore.ensure_index(field) def test_gfs_metadata(gridfsstore): """ Ensure metadata is put back in the document """ tic = datetime(2018, 4, 12, 16) gridfsstore.ensure_metadata = True for i in range(3): data = { "a": 1, } metadata = {"task_id": f"mp-{i}", "a": 1, gridfsstore.last_updated_field: tic} data = json.dumps(data).encode("UTF-8") gridfsstore._collection.put(data, metadata=metadata) for d in gridfsstore.query(): assert "task_id" in d assert gridfsstore.last_updated_field in d def test_gridfsstore_from_launchpad_file(lp_file): ms = GridFSStore.from_launchpad_file(lp_file, collection_name="tmp") ms.connect() assert ms.name == "gridfs://localhost/maggma_tests/tmp" def test_searchable_fields(gridfsstore): tic = datetime(2018, 4, 12, 16) data = [{"task_id": f"mp-{i}", "a": i, gridfsstore.last_updated_field: tic} for i in range(3)] gridfsstore.searchable_fields = ["task_id"] gridfsstore.update(data, key="a") # This should only work if the searchable field was put into the index store assert set(gridfsstore.distinct("task_id")) == {"mp-0", "mp-1", "mp-2"} def test_additional_metadata(gridfsstore): tic = datetime(2018, 4, 12, 16) data = [{"task_id": f"mp-{i}", "a": i, gridfsstore.last_updated_field: tic} for i in range(3)] gridfsstore.update(data, key="a", additional_metadata="task_id") # This should only work if the searchable field was put into the index store assert set(gridfsstore.distinct("task_id")) == {"mp-0", "mp-1", "mp-2"} @pytest.mark.skipif( "mongodb+srv" not in os.environ.get("MONGODB_SRV_URI", ""), reason="requires special mongodb+srv URI", ) def test_gridfs_uri(): uri = os.environ["MONGODB_SRV_URI"] store = GridFSURIStore(uri, database="mp_core", collection_name="xas") store.connect() is_name = store.name is uri # This is try and keep the secret safe assert is_name def test_gridfs_uri_dbname_parse(): # test parsing dbname from uri uri_with_db = "mongodb://uuu:xxxx@host:27017/fake_db" store = GridFSURIStore(uri_with_db, "test") assert store.database == "fake_db" uri_with_db = "mongodb://uuu:xxxx@host:27017/fake_db" store = GridFSURIStore(uri_with_db, "test", database="fake_db2") assert store.database == "fake_db2" uri_with_db = "mongodb://uuu:xxxx@host:27017" with pytest.raises(ConfigurationError): GridFSURIStore(uri_with_db, "test") def test_close(gridfsstore): assert gridfsstore.query_one() is None gridfsstore.close() with pytest.raises(StoreError): gridfsstore.query_one() # reconnect to allow the drop of the collection in the fixture gridfsstore.connect()