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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()
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