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import os
import shutil
from datetime import datetime
from pathlib import Path
from unittest import mock
import mongomock.collection
import orjson
import pymongo.collection
import pytest
from bson.objectid import ObjectId
from monty.tempfile import ScratchDir
from pymongo.errors import ConfigurationError, DocumentTooLarge, OperationFailure
from maggma.core import StoreError
from maggma.stores import JSONStore, MemoryStore, MongoStore, MongoURIStore, MontyStore
from maggma.validators import JSONSchemaValidator
@pytest.fixture()
def mongostore():
store = MongoStore(
database="maggma_test",
collection_name="test",
)
store.connect()
yield store
store._collection.drop()
@pytest.fixture()
def montystore(tmp_dir):
store = MontyStore("maggma_test")
store.connect()
return store
@pytest.fixture()
def memorystore():
store = MemoryStore()
store.connect()
return store
@pytest.fixture()
def jsonstore(test_dir):
files = []
for f in ["a.json", "b.json"]:
files.append(test_dir / "test_set" / f)
return JSONStore(files)
@pytest.mark.xfail(raises=StoreError)
def test_mongostore_connect_error():
mongostore = MongoStore("maggma_test", "test")
mongostore.count()
def test_mongostore_connect_reconnect():
mongostore = MongoStore("maggma_test", "test")
assert mongostore._coll is None
mongostore.connect()
assert isinstance(mongostore._collection, pymongo.collection.Collection)
mongostore.close()
assert mongostore._coll is None
mongostore.connect()
def test_mongostore_query(mongostore):
mongostore._collection.insert_one({"a": 1, "b": 2, "c": 3})
assert mongostore.query_one(properties=["a"])["a"] == 1
assert mongostore.query_one(properties=["a"])["a"] == 1
assert mongostore.query_one(properties=["b"])["b"] == 2
assert mongostore.query_one(properties=["c"])["c"] == 3
def test_mongostore_count(mongostore):
mongostore._collection.insert_one({"a": 1, "b": 2, "c": 3})
assert mongostore.count() == 1
mongostore._collection.insert_one({"aa": 1, "b": 2, "c": 3})
assert mongostore.count() == 2
assert mongostore.count({"a": 1}) == 1
def test_mongostore_distinct(mongostore):
mongostore._collection.insert_one({"a": 1, "b": 2, "c": 3})
mongostore._collection.insert_one({"a": 4, "d": 5, "e": 6, "g": {"h": 1}})
assert set(mongostore.distinct("a")) == {1, 4}
# Test list distinct functionality
mongostore._collection.insert_one({"a": 4, "d": 6, "e": 7})
mongostore._collection.insert_one({"a": 4, "d": 6, "g": {"h": 2}})
# Test distinct subdocument functionality
ghs = mongostore.distinct("g.h")
assert set(ghs) == {1, 2}
# Test when key doesn't exist
assert mongostore.distinct("blue") == []
# Test when null is a value
mongostore._collection.insert_one({"i": None})
assert mongostore.distinct("i") == [None]
# Test to make sure DocumentTooLarge errors get dealt with properly using built in distinct
mongostore._collection.insert_many([{"key": [f"mp-{i}"]} for i in range(1000000)])
vals = mongostore.distinct("key")
# Test to make sure distinct on array field is unraveled when using manual distinct
assert len(vals) == len(list(range(1000000)))
assert all(isinstance(v, str) for v in vals)
# Test to make sure manual distinct uses the criteria query
mongostore._collection.insert_many([{"key": f"mp-{i}", "a": 2} for i in range(1000001, 2000001)])
vals = mongostore.distinct("key", {"a": 2})
assert len(vals) == len(list(range(1000001, 2000001)))
def test_mongostore_update(mongostore):
mongostore.update({"e": 6, "d": 4}, key="e")
assert mongostore.query_one(criteria={"d": {"$exists": 1}}, properties=["d"])["d"] == 4
mongostore.update([{"e": 7, "d": 8, "f": 9}], key=["d", "f"])
assert mongostore.query_one(criteria={"d": 8, "f": 9}, properties=["e"])["e"] == 7
mongostore.update([{"e": 11, "d": 8, "f": 9}], key=["d", "f"])
assert mongostore.query_one(criteria={"d": 8, "f": 9}, properties=["e"])["e"] == 11
test_schema = {
"type": "object",
"properties": {"e": {"type": "integer"}},
"required": ["e"],
}
mongostore.validator = JSONSchemaValidator(schema=test_schema)
mongostore.update({"e": 100, "d": 3}, key="e")
# Continue to update doc when validator is not set to strict mode
mongostore.update({"e": "abc", "d": 3}, key="e")
# ensure safe_update works to not throw DocumentTooLarge errors
large_doc = {f"mp-{i}": f"mp-{i}" for i in range(1000000)}
large_doc["e"] = 999
with pytest.raises((OperationFailure, DocumentTooLarge)):
mongostore.update([large_doc, {"e": 1001}], key="e")
mongostore.safe_update = True
mongostore.update([large_doc, {"e": 1001}], key="e")
assert mongostore.query_one({"e": 1001}) is not None
def test_mongostore_groupby(mongostore):
mongostore.update(
[
{"e": 7, "d": 9, "f": 9},
{"e": 7, "d": 9, "f": 10},
{"e": 8, "d": 9, "f": 11},
{"e": 9, "d": 10, "f": 12},
],
key="f",
)
data = list(mongostore.groupby("d"))
assert len(data) == 2
grouped_by_9 = next(g[1] for g in data if g[0]["d"] == 9)
assert len(grouped_by_9) == 3
grouped_by_10 = next(g[1] for g in data if g[0]["d"] == 10)
assert len(grouped_by_10) == 1
data = list(mongostore.groupby(["e", "d"]))
assert len(data) == 3
def test_mongostore_remove_docs(mongostore):
mongostore._collection.insert_one({"a": 1, "b": 2, "c": 3})
mongostore._collection.insert_one({"a": 4, "d": 5, "e": 6, "g": {"h": 1}})
mongostore.remove_docs({"a": 1})
assert len(list(mongostore.query({"a": 4}))) == 1
assert len(list(mongostore.query({"a": 1}))) == 0
def test_mongostore_from_db_file(mongostore, db_json):
ms = MongoStore.from_db_file(db_json)
ms.connect()
assert ms._collection.full_name == "maggma_tests.tmp"
def test_mongostore_from_launchpad_file(lp_file):
ms = MongoStore.from_launchpad_file(lp_file, collection_name="tmp")
ms.connect()
assert ms._collection.full_name == "maggma_tests.tmp"
def test_mongostore_from_collection(mongostore, db_json):
ms = MongoStore.from_db_file(db_json)
ms.connect()
other_ms = MongoStore.from_collection(ms._collection)
assert ms._coll.full_name == other_ms._collection.full_name
assert ms.database == other_ms.database
def test_mongostore_name(mongostore):
assert mongostore.name == "mongo://localhost/maggma_test/test"
def test_ensure_index(mongostore):
assert mongostore.ensure_index("test_key")
# TODO: How to check for exception?
def test_mongostore_last_updated(mongostore):
assert mongostore.last_updated == datetime.min
start_time = datetime.utcnow()
mongostore._collection.insert_one({mongostore.key: 1, "a": 1})
with pytest.raises(StoreError) as cm: # noqa: PT012
mongostore.last_updated # noqa: B018
assert cm.match(mongostore.last_updated_field)
mongostore.update([{mongostore.key: 1, "a": 1, mongostore.last_updated_field: datetime.utcnow()}])
assert mongostore.last_updated > start_time
def test_mongostore_newer_in(mongostore):
target = MongoStore("maggma_test", "test_target")
target.connect()
# make sure docs are newer in mongostore then target and check updated_keys
target.update([{mongostore.key: i, mongostore.last_updated_field: datetime.utcnow()} for i in range(10)])
# Update docs in source
mongostore.update([{mongostore.key: i, mongostore.last_updated_field: datetime.utcnow()} for i in range(10)])
assert len(target.newer_in(mongostore)) == 10
assert len(target.newer_in(mongostore, exhaustive=True)) == 10
assert len(mongostore.newer_in(target)) == 0
target._collection.drop()
# Memory store tests
def test_memory_store_connect():
memorystore = MemoryStore()
assert memorystore._coll is None
memorystore.connect()
assert isinstance(memorystore._collection, mongomock.collection.Collection)
def test_groupby(memorystore):
memorystore.update(
[
{"e": 7, "d": 9, "f": 9},
{"e": 7, "d": 9, "f": 10},
{"e": 8, "d": 9, "f": 11},
{"e": 9, "d": 10, "f": 12},
],
key="f",
)
data = list(memorystore.groupby("d", properties={"e": 1, "f": 1}))
assert len(data) == 2
grouped_by_9 = next(g[1] for g in data if g[0]["d"] == 9)
assert len(grouped_by_9) == 3
assert all(d.get("f", False) for d in grouped_by_9)
assert all(d.get("e", False) for d in grouped_by_9)
grouped_by_10 = next(g[1] for g in data if g[0]["d"] == 10)
assert len(grouped_by_10) == 1
data = list(memorystore.groupby(["e", "d"]))
assert len(data) == 3
memorystore.update(
[
{"e": {"d": 9}, "f": 9},
{"e": {"d": 9}, "f": 10},
{"e": {"d": 9}, "f": 11},
{"e": {"d": 10}, "f": 12},
],
key="f",
)
data = list(memorystore.groupby("e.d", properties=["f"]))
assert len(data) == 2
assert data[0][1][0].get("f", False)
# Monty store tests
def test_monty_store_connect(tmp_dir):
montystore = MontyStore(collection_name="my_collection")
assert montystore._coll is None
montystore.connect()
assert montystore._collection is not None
assert montystore.name is not None
# check that the kwargs work
with ScratchDir("."):
store = MontyStore("my_results", database_name="NotNamedDB")
store.connect()
store.update({"test": {"cow": "moo"}}, key="test")
store.close()
assert Path("NotNamedDB/my_results.collection").exists()
def test_monty_store_groupby(montystore):
montystore.update(
[
{"e": 7, "d": 9, "f": 9},
{"e": 7, "d": 9, "f": 10},
{"e": 8, "d": 9, "f": 11},
{"e": 9, "d": 10, "f": 12},
],
key="f",
)
data = list(montystore.groupby("d"))
assert len(data) == 2
grouped_by_9 = next(g[1] for g in data if g[0]["d"] == 9)
assert len(grouped_by_9) == 3
grouped_by_10 = next(g[1] for g in data if g[0]["d"] == 10)
assert len(grouped_by_10) == 1
data = list(montystore.groupby(["e", "d"]))
assert len(data) == 3
montystore.update(
[
{"e": {"d": 9}, "f": 9},
{"e": {"d": 9}, "f": 10},
{"e": {"d": 9}, "f": 11},
{"e": {"d": 10}, "f": 12},
],
key="f",
)
data = list(montystore.groupby("e.d"))
assert len(data) == 2
def test_monty_store_query(montystore):
montystore._collection.insert_one({"a": 1, "b": 2, "c": 3})
assert montystore.query_one(properties=["a"])["a"] == 1
assert montystore.query_one(properties=["a"])["a"] == 1
assert montystore.query_one(properties=["b"])["b"] == 2
assert montystore.query_one(properties=["c"])["c"] == 3
def test_monty_store_count(montystore):
montystore._collection.insert_one({"a": 1, "b": 2, "c": 3})
assert montystore.count() == 1
montystore._collection.insert_one({"aa": 1, "b": 2, "c": 3})
assert montystore.count() == 2
assert montystore.count({"a": 1}) == 1
def test_monty_store_distinct(montystore):
montystore._collection.insert_one({"a": 1, "b": 2, "c": 3})
montystore._collection.insert_one({"a": 4, "d": 5, "e": 6, "g": {"h": 1}})
assert set(montystore.distinct("a")) == {1, 4}
# Test list distinct functionality
montystore._collection.insert_one({"a": 4, "d": 6, "e": 7})
montystore._collection.insert_one({"a": 4, "d": 6, "g": {"h": 2}})
# Test distinct subdocument functionality
ghs = montystore.distinct("g.h")
assert set(ghs) == {1, 2}
# Test when key doesn't exist
assert montystore.distinct("blue") == []
# Test when null is a value
montystore._collection.insert_one({"i": None})
assert montystore.distinct("i") == [None]
def test_monty_store_update(montystore):
montystore.update({"e": 6, "d": 4}, key="e")
assert montystore.query_one(criteria={"d": {"$exists": 1}}, properties=["d"])["d"] == 4
montystore.update([{"e": 7, "d": 8, "f": 9}], key=["d", "f"])
assert montystore.query_one(criteria={"d": 8, "f": 9}, properties=["e"])["e"] == 7
montystore.update([{"e": 11, "d": 8, "f": 9}], key=["d", "f"])
assert montystore.query_one(criteria={"d": 8, "f": 9}, properties=["e"])["e"] == 11
test_schema = {
"type": "object",
"properties": {"e": {"type": "integer"}},
"required": ["e"],
}
montystore.validator = JSONSchemaValidator(schema=test_schema)
montystore.update({"e": 100, "d": 3}, key="e")
# Continue to update doc when validator is not set to strict mode
montystore.update({"e": "abc", "d": 3}, key="e")
def test_monty_store_remove_docs(montystore):
montystore._collection.insert_one({"a": 1, "b": 2, "c": 3})
montystore._collection.insert_one({"a": 4, "d": 5, "e": 6, "g": {"h": 1}})
montystore.remove_docs({"a": 1})
assert len(list(montystore.query({"a": 4}))) == 1
assert len(list(montystore.query({"a": 1}))) == 0
def test_monty_store_last_updated(montystore):
assert montystore.last_updated == datetime.min
start_time = datetime.utcnow()
montystore._collection.insert_one({montystore.key: 1, "a": 1})
with pytest.raises(StoreError) as cm: # noqa: PT012
montystore.last_updated # noqa: B018
assert cm.match(montystore.last_updated_field)
montystore.update([{montystore.key: 1, "a": 1, montystore.last_updated_field: datetime.utcnow()}])
assert montystore.last_updated > start_time
def test_json_store_load(jsonstore, test_dir):
jsonstore.connect()
assert len(list(jsonstore.query())) == 20
jsonstore = JSONStore(test_dir / "test_set" / "c.json.gz")
jsonstore.connect()
assert len(list(jsonstore.query())) == 20
# test with non-default encoding
jsonstore = JSONStore(test_dir / "test_set" / "c.json.gz", encoding="utf8")
jsonstore.connect()
assert len(list(jsonstore.query())) == 20
# confirm descriptive error raised if you get a KeyError
jsonstore = JSONStore(test_dir / "test_set" / "c.json.gz", key="random_key")
with pytest.raises(KeyError, match="Key field 'random_key' not found"):
jsonstore.connect()
# if the .json does not exist, it should be created
with pytest.warns(DeprecationWarning, match="file_writable is deprecated"):
jsonstore = JSONStore("a.json", file_writable=False)
assert jsonstore.read_only is True
# test loading an extended JSON file exported from MongoDB
js2 = JSONStore(test_dir / "test_set" / "extended_json.json")
js2.connect()
assert js2.count() == 1
assert js2.query_one()["_id"] == ObjectId("64ebee18bd0b1265fe418be2")
def test_json_store_writeable(test_dir):
with ScratchDir("."):
# if the .json does not exist, it should be created
jsonstore = JSONStore("a.json", read_only=False)
jsonstore.connect()
assert Path("a.json").exists()
# confirm RunTimeError with multiple paths
with pytest.raises(RuntimeError, match="multiple JSON"):
jsonstore = JSONStore(["a.json", "d.json"], read_only=False)
shutil.copy(test_dir / "test_set" / "d.json", ".")
jsonstore = JSONStore("d.json", read_only=False)
jsonstore.connect()
assert jsonstore.count() == 2
jsonstore.update({"new": "hello", "task_id": 2})
assert jsonstore.count() == 3
jsonstore.close()
# repeat the above with the deprecated file_writable kwarg
# if the .json does not exist, it should be created
with pytest.warns(UserWarning, match="Received conflicting keyword arguments"):
jsonstore = JSONStore("a.json", file_writable=True)
assert jsonstore.read_only is False
assert Path("a.json").exists()
jsonstore.connect()
# confirm RunTimeError with multiple paths
with pytest.raises(RuntimeError, match="multiple JSON"):
jsonstore = JSONStore(["a.json", "d.json"], file_writable=True)
shutil.copy(test_dir / "test_set" / "d.json", ".")
jsonstore = JSONStore("d.json", file_writable=True)
jsonstore.connect()
assert jsonstore.count() == 2
jsonstore.update({"new": "hello", "task_id": 2})
assert jsonstore.count() == 3
jsonstore.close()
jsonstore = JSONStore("d.json", file_writable=True)
jsonstore.connect()
assert jsonstore.count() == 3
jsonstore.remove_docs({"a": 5})
assert jsonstore.count() == 2
jsonstore.close()
jsonstore = JSONStore("d.json", file_writable=True)
jsonstore.connect()
assert jsonstore.count() == 2
jsonstore.close()
with mock.patch("maggma.stores.JSONStore.update_json_file") as update_json_file_mock:
jsonstore = JSONStore("d.json", file_writable=False)
jsonstore.connect()
jsonstore.update({"new": "hello", "task_id": 5})
assert jsonstore.count() == 3
jsonstore.close()
update_json_file_mock.assert_not_called()
with mock.patch("maggma.stores.JSONStore.update_json_file") as update_json_file_mock:
jsonstore = JSONStore("d.json", file_writable=False)
jsonstore.connect()
jsonstore.remove_docs({"task_id": 5})
assert jsonstore.count() == 2
jsonstore.close()
update_json_file_mock.assert_not_called()
def test_jsonstore_orjson_options(test_dir):
class SubFloat(float):
pass
with ScratchDir("."):
jsonstore = JSONStore("d.json", read_only=False)
jsonstore.connect()
with pytest.raises(orjson.JSONEncodeError):
jsonstore.update({"wrong_field": SubFloat(1.1), "task_id": 3})
jsonstore.close()
jsonstore = JSONStore(
"a.json",
read_only=False,
serialization_option=None,
serialization_default=lambda x: "test",
)
jsonstore.connect()
jsonstore.update({"wrong_field": SubFloat(1.1), "task_id": 3})
jsonstore.close()
def test_jsonstore_last_updated(test_dir):
# files = []
# for f in ["a.json", "b.json"]:
# files.append(test_dir / "test_set" / f)
with ScratchDir("."):
# if the .json does not exist, it should be created
jsonstore = JSONStore("a.json", read_only=False)
jsonstore.connect()
start_time = datetime.utcnow()
# NOTE: mongo only stores datetime with ms precision (apparently), and that
# can cause the test below to fail. So we add a wait here.
import time
time.sleep(0.1)
jsonstore.update(
[
{
jsonstore.key: 1,
"a": 1,
jsonstore.last_updated_field: datetime.utcnow(),
}
]
)
# These lines ensure that the read_json_file method gets called after
# last_updated is written to the .json file
jsonstore.close()
jsonstore.connect()
assert jsonstore.last_updated > start_time
def test_eq(mongostore, memorystore, jsonstore):
assert mongostore == mongostore
assert memorystore == memorystore
assert jsonstore == jsonstore
assert mongostore != memorystore
assert mongostore != jsonstore
assert memorystore != jsonstore
@pytest.mark.skipif(
"mongodb+srv" not in os.environ.get("MONGODB_SRV_URI", ""),
reason="requires special mongodb+srv URI",
)
def test_mongo_uri():
uri = os.environ["MONGODB_SRV_URI"]
store = MongoURIStore(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_mongo_uri_localhost():
store = MongoURIStore("mongodb://localhost:27017/mp_core", collection_name="xas")
store.connect()
def test_mongo_uri_dbname_parse():
# test parsing dbname from uri
uri_with_db = "mongodb://uuu:xxxx@host:27017/fake_db"
store = MongoURIStore(uri_with_db, "test")
assert store.database == "fake_db"
uri_with_db = "mongodb://uuu:xxxx@host:27017/fake_db"
store = MongoURIStore(uri_with_db, "test", database="fake_db2")
assert store.database == "fake_db2"
uri_with_db = "mongodb://uuu:xxxx@host:27017"
with pytest.raises(ConfigurationError):
MongoURIStore(uri_with_db, "test")
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