1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616
|
import gzip
import pickle
from datetime import datetime, timedelta
from io import BytesIO, StringIO
import boto3
import jsonlines
import pandas as pd
import pytest
from bson import json_util
from moto import mock_aws
from maggma.stores.open_data import OpenDataStore, PandasMemoryStore, S3IndexStore, TasksOpenDataStore
pd.set_option("future.no_silent_downcasting", True)
# PandasMemoryStore tests
@pytest.fixture()
def memstore():
store = PandasMemoryStore(key="task_id")
store.update(
pd.DataFrame(
[
{
store.key: "mp-1",
store.last_updated_field: datetime.utcnow(),
"data": "asd",
"int_val": 1,
},
{
store.key: "mp-3",
store.last_updated_field: datetime.utcnow(),
"data": "sdf",
"int_val": 3,
},
]
)
)
return store
def test_pdmems_pickle(memstore):
sobj = pickle.dumps(memstore)
dobj = pickle.loads(sobj)
assert hash(dobj) == hash(memstore)
assert dobj == memstore
def test_pdmems_query(memstore):
# bad criteria
with pytest.raises(AttributeError, match=r".*only support query or is_in"):
memstore.query(criteria={"boo": "hoo"})
with pytest.raises(AttributeError, match=r".*please just use one or the other"):
memstore.query(
criteria={
"query": f"{memstore.key} == 'mp-1'",
"is_in": ("data", ["sdf", "fdr"]),
"boo": "hoo",
}
)
# all
pd = memstore.query()
assert len(pd) == 2
# query criteria
pd = memstore.query(criteria={"query": f"{memstore.key} == 'mp-1'"})
assert len(pd) == 1
assert pd[memstore.key].iloc[0] == "mp-1"
assert pd["data"].iloc[0] == "asd"
# is_in criteria
pd = memstore.query(criteria={"is_in": ("data", ["sdf", "fdr"]), "boo": "hoo"})
assert len(pd) == 1
assert pd[memstore.key].iloc[0] == "mp-3"
assert pd["data"].iloc[0] == "sdf"
# properties
pd = memstore.query(properties=[memstore.key, memstore.last_updated_field])
assert len(pd) == 2
assert len(pd[memstore.key]) == 2
with pytest.raises(KeyError):
assert pd["data"]
with pytest.raises(KeyError):
memstore.query(properties=["fake"])
# sort
pd = memstore.query(sort={memstore.key: -1})
assert len(pd) == 2
assert pd[memstore.key].iloc[0] == "mp-3"
# skip
pd = memstore.query(sort={memstore.key: -1}, skip=1)
assert len(pd) == 1
assert pd[memstore.key].iloc[0] == "mp-1"
# limit
pd = memstore.query(sort={memstore.key: -1}, limit=1)
assert len(pd) == 1
assert pd[memstore.key].iloc[0] == "mp-3"
# all
pd = memstore.query(
criteria={
"is_in": ("data", ["sdf", "fdr", "asd"]),
"boo": "hoo",
},
properties=[memstore.key],
sort={"data": -1},
skip=1,
limit=1,
)
assert len(pd) == 1
assert pd[memstore.key].iloc[0] == "mp-1"
with pytest.raises(KeyError):
assert pd["data"]
def test_pdmems_count(memstore):
assert memstore.count() == 2
assert memstore.count(criteria={"query": f"{memstore.key} == 'mp-1'"}) == 1
assert memstore.count(criteria={"is_in": ("data", ["sdf", "fdr"]), "boo": "hoo"}) == 1
assert PandasMemoryStore(key="task_id").count() == 0
@pytest.fixture()
def memstore2():
store = PandasMemoryStore(key="task_id")
store.update(
pd.DataFrame(
[
{
store.key: "mp-1",
store.last_updated_field: datetime.utcnow() - timedelta(hours=1),
"data": "asd",
},
{
store.key: "mp-2",
store.last_updated_field: datetime.utcnow() + timedelta(hours=1),
"data": "asd",
},
{
store.key: "mp-3",
store.last_updated_field: datetime.utcnow() + timedelta(hours=1),
"data": "sdf",
},
]
)
)
return store
def test_pdmems_distinct(memstore2):
assert len(memstore2.distinct(field=memstore2.key)) == len(memstore2._data)
assert len(memstore2.distinct(field="data")) == 2
assert len(memstore2.distinct(field=memstore2.key, criteria={"query": "data == 'asd'"})) == 2
def test_pdmems_last_updated(memstore2):
assert memstore2._data[memstore2.last_updated_field].iloc[2] == memstore2.last_updated
store = PandasMemoryStore(key="task_id")
assert store.last_updated == datetime.min
def test_pdmems_newer_in(memstore, memstore2):
s = memstore.newer_in(memstore2)
assert len(s) == 2
assert "mp-2" in s.unique()
assert "mp-3" in s.unique()
s = memstore.newer_in(target=memstore2, criteria={"query": "data == 'asd'"}, exhaustive=True)
assert len(s) == 1
assert "mp-2" in s.unique()
with pytest.raises(AttributeError):
memstore.newer_in(target=memstore2, criteria={"query": "data == 'asd'"}, exhaustive=False)
def test_pdmems_update(memstore):
df = pd.DataFrame(
[
{
memstore.key: "mp-1",
memstore.last_updated_field: datetime.utcnow(),
"data": "boo",
"int_val": 1,
}
]
)
df2 = memstore.update(df)
assert len(memstore._data) == 2
assert memstore.query(criteria={"query": f"{memstore.key} == 'mp-1'"})["data"].iloc[0] == "boo"
assert memstore.query(criteria={"query": f"{memstore.key} == 'mp-1'"})["int_val"].iloc[0] == 1
assert df2.equals(df)
df = pd.DataFrame(
[
{
memstore.key: "mp-2",
memstore.last_updated_field: datetime.utcnow(),
"data": "boo",
"int_val": 2,
}
]
)
df2 = memstore.update(df)
assert len(memstore._data) == 3
assert memstore.query(criteria={"query": f"{memstore.key} == 'mp-2'"})["data"].iloc[0] == "boo"
assert memstore.query(criteria={"query": f"{memstore.key} == 'mp-2'"})["int_val"].iloc[0] == 2
assert df2.equals(df)
@pytest.fixture()
def s3indexstore():
data = [{"task_id": "mp-1", "last_updated": datetime.utcnow()}]
with mock_aws():
conn = boto3.resource("s3", region_name="us-east-1")
conn.create_bucket(Bucket="bucket1")
client = boto3.client("s3", region_name="us-east-1")
string_io = StringIO()
with jsonlines.Writer(string_io, dumps=json_util.dumps) as writer:
for _, row in pd.DataFrame(data).iterrows():
writer.write(row.to_dict())
client.put_object(
Bucket="bucket1",
Body=BytesIO(string_io.getvalue().encode("utf-8")),
Key="manifest.jsonl",
)
store = S3IndexStore(collection_name="index", bucket="bucket1", key="task_id")
store.connect()
yield store
def test_s3is_pickle(s3indexstore):
sobj = pickle.dumps(s3indexstore)
dobj = pickle.loads(sobj)
assert hash(dobj) == hash(s3indexstore)
assert dobj == s3indexstore
def test_s3is_connect_retrieve_manifest(s3indexstore):
assert s3indexstore.retrieve_manifest().equals(s3indexstore._data)
with mock_aws():
with pytest.raises(s3indexstore.s3_client.exceptions.NoSuchBucket):
S3IndexStore(collection_name="foo", bucket="bucket2", key="task_id").retrieve_manifest()
with pytest.raises(RuntimeError):
S3IndexStore(collection_name="foo", bucket="bucket2", key="task_id").connect()
conn = boto3.resource("s3", region_name="us-east-1")
conn.create_bucket(Bucket="bucket2")
s3is = S3IndexStore(collection_name="foo", bucket="bucket2", key="task_id")
s3is.connect()
assert s3is._data is None
assert s3is.retrieve_manifest() is None
assert s3is.count() == 0
def test_s3is_store_manifest():
with mock_aws():
conn = boto3.resource("s3", region_name="us-east-1")
conn.create_bucket(Bucket="bucket2")
s3is = S3IndexStore(collection_name="foo", bucket="bucket2", key="task_id")
s3is.connect()
s3is.update(pd.DataFrame([{"task_id": "mp-2", "last_updated": "now"}]))
s3is.store_manifest()
df = s3is.retrieve_manifest()
assert len(df) == 1
assert df.equals(s3is._data)
s3is.update(pd.DataFrame([{"task_id": "mp-3", "last_updated": "later"}]))
df = s3is.retrieve_manifest()
assert not df.equals(s3is._data)
def test_s3is_close(s3indexstore):
s3indexstore.close()
assert len(s3indexstore.query()) == 1 # actions auto-reconnect
s3indexstore.update(pd.DataFrame([{"task_id": "mp-2", "last_updated": "now"}]))
assert len(s3indexstore.query()) == 2
s3indexstore.close()
assert len(s3indexstore.query()) == 2 # actions auto-reconnect
s3indexstore.close()
s3indexstore.connect()
assert len(s3indexstore.query()) == 1 # explicit connect reloads manifest
@pytest.fixture()
def s3store():
with mock_aws():
conn = boto3.resource("s3", region_name="us-east-1")
conn.create_bucket(Bucket="bucket1")
store = OpenDataStore(
collection_name="index", bucket="bucket1", key="task_id", object_grouping=["group_level_two", "task_id"]
)
store.connect()
store.update(
pd.DataFrame(
[
{
"task_id": "mp-1",
"data": "asd",
store.last_updated_field: datetime.utcnow(),
"group": {"level_two": 4},
},
{
"task_id": "mp-3",
"data": "sdf",
store.last_updated_field: datetime.utcnow(),
"group": {"level_two": 4},
},
]
)
)
yield store
@pytest.fixture()
def s3store_w_subdir():
with mock_aws():
conn = boto3.resource("s3", region_name="us-east-1")
conn.create_bucket(Bucket="bucket1")
conn.create_bucket(Bucket="bucket2")
index = S3IndexStore(collection_name="index", bucket="bucket1", key="task_id")
store = OpenDataStore(
index=index,
collection_name=index.collection_name,
bucket="bucket2",
key=index.key,
prefix="subdir1",
object_grouping=["data_foo"],
)
store.connect()
store.update(
pd.DataFrame(
[
{
"task_id": "mp-1",
"data": {"foo": "asd"},
store.last_updated_field: datetime.utcnow(),
},
{
"task_id": "mp-3",
"data": {"foo": "sdf"},
store.last_updated_field: datetime.utcnow(),
},
]
)
)
yield store
def test_pickle(s3store):
sobj = pickle.dumps(s3store)
dobj = pickle.loads(sobj)
assert hash(dobj) == hash(s3store)
assert dobj == s3store
assert len(dobj.query(criteria={"query": "task_id == 'mp-2'"})) == 0
assert dobj.query(criteria={"query": "task_id == 'mp-1'"})["data"].iloc[0] == "asd"
def test_index_property(s3store, s3store_w_subdir):
assert s3store.index != s3store
assert s3store_w_subdir.index != s3store_w_subdir
def test_read_doc_from_s3():
data = [
{"task_id": "mp-1", "last_updated": datetime.utcnow(), "group": "foo", "also_group": "boo"},
{"task_id": "mp-2", "last_updated": datetime.utcnow(), "group": "foo", "also_group": "boo"},
]
with mock_aws():
conn = boto3.resource("s3", region_name="us-east-1")
conn.create_bucket(Bucket="bucket1")
client = boto3.client("s3", region_name="us-east-1")
string_io = StringIO()
with jsonlines.Writer(string_io, dumps=json_util.dumps) as writer:
for _, row in pd.DataFrame(data).iterrows():
writer.write(row.to_dict())
client.put_object(
Bucket="bucket1",
Body=BytesIO(gzip.compress(string_io.getvalue().encode("utf-8"))),
Key="group=foo/also_group=boo.jsonl.gz",
)
store = OpenDataStore(
collection_name="index", bucket="bucket1", key="task_id", object_grouping=["group", "also_group"]
)
store.connect()
df = store._read_doc_from_s3(file_id="group=foo/also_group=boo.jsonl.gz")
assert len(df) == 2
assert store._get_full_key_path(index=df) == "group=foo/also_group=boo.jsonl.gz"
assert (df["task_id"] == "mp-1").any()
assert (df["task_id"] == "mp-2").any()
@pytest.mark.xfail(
reason="Known issue, the store is in a deprecated state, and in particular may be incompatible with numpy 2.0+"
)
def test_update(s3store):
assert len(s3store.index_data) == 2
s3store.update(
pd.DataFrame(
[
{
"task_id": "mp-199999",
"data": "asd",
"group": {"level_two": 4},
s3store.last_updated_field: datetime.utcnow(),
}
]
)
)
assert len(s3store.index_data) == 3
with pytest.raises(KeyError):
assert s3store.index_data.query("task_id == 'mp-199999'")["data"].iloc[0] == "asd"
s3store.update(
pd.DataFrame(
[
{
"task_id": "mp-199999",
"data": "foo",
"group": {"level_two": 4},
s3store.last_updated_field: datetime.utcnow(),
}
]
)
)
assert len(s3store.index_data) == 3
assert len(s3store.index_data.query("task_id == 'mp-199999'")) == 1
mp4 = [{"task_id": "mp-4", "data": "asd", "group": {"level_two": 4}, s3store.last_updated_field: datetime.utcnow()}]
s3store.update(pd.DataFrame(mp4))
assert len(s3store.index_data) == 4
mp4_index = [{"task_id": "mp-4", "group_level_two": 4, s3store.last_updated_field: datetime.utcnow()}]
assert s3store._get_full_key_path(pd.DataFrame(mp4_index)) == "group_level_two=4/task_id=mp-4.jsonl.gz"
s3store.s3_client.head_object(Bucket=s3store.bucket, Key=s3store._get_full_key_path(pd.DataFrame(mp4_index)))
def test_query(s3store):
assert len(s3store.query(criteria={"query": "task_id == 'mp-2'"})) == 0
assert s3store.query(criteria={"query": "task_id == 'mp-1'"})["data"].iloc[0] == "asd"
assert s3store.query(criteria={"query": "task_id == 'mp-3'"})["data"].iloc[0] == "sdf"
assert s3store.query(criteria={"query": "task_id == 'mp-1'"}, properties=["task_id"])["task_id"].iloc[0] == "mp-1"
assert (
s3store.query(criteria={"query": "task_id == 'mp-1'"}, properties=["task_id", "data"])["data"].iloc[0] == "asd"
)
assert len(s3store.query()) == 2
# will use optimized search
df = s3store.query(criteria={"query": "task_id == 'mp-1'"}, properties=["task_id"], criteria_fields=["task_id"])
assert len(df) == 1
assert df["task_id"].iloc[0] == "mp-1"
with pytest.raises(KeyError):
assert df["data"].iloc[0] == "asd"
# will use optimized search
df = s3store.query(properties=["task_id"], criteria_fields=[])
assert len(df) == 2
# will not use optimized search even with hints since data is not in the searchable_fields
df = s3store.query(criteria={"query": "data == 'asd'"}, properties=["task_id"], criteria_fields=["data"])
assert len(df) == 1
assert df["task_id"].iloc[0] == "mp-1"
with pytest.raises(KeyError):
assert df["data"].iloc[0] == "asd"
def test_rebuild_index_from_s3_data(s3store):
data = [
{"task_id": "mp-2", "data": "asd", s3store.last_updated_field: datetime.utcnow(), "group": {"level_two": 4}}
]
client = boto3.client("s3", region_name="us-east-1")
string_io = StringIO()
with jsonlines.Writer(string_io, dumps=json_util.dumps) as writer:
for _, row in pd.DataFrame(data).iterrows():
writer.write(row.to_dict())
data = [
{"task_id": "mp-99", "data": "asd", s3store.last_updated_field: datetime.utcnow(), "group": {"level_two": 4}}
]
string_io2 = StringIO()
with jsonlines.Writer(string_io2, dumps=json_util.dumps) as writer:
for _, row in pd.DataFrame(data).iterrows():
writer.write(row.to_dict())
client.put_object(
Bucket="bucket1",
Body=BytesIO(gzip.compress(string_io.getvalue().encode("utf-8"))),
Key="group_level_two=4/task_id=mp-2.jsonl.gz",
)
# creating file that should not be indexed to test that it gets skipped
client.put_object(
Bucket="bucket1",
Body=BytesIO(gzip.compress(string_io2.getvalue().encode("utf-8"))),
Key="task_id=mp-99.gz",
)
assert len(s3store.index.index_data) == 2
index_docs = s3store.rebuild_index_from_s3_data()
assert len(index_docs) == 3
assert len(s3store.index.index_data) == 3
for key in index_docs.columns:
assert key == "task_id" or key == "last_updated" or key == "group_level_two"
def test_rebuild_index_from_data(s3store):
data = [
{"task_id": "mp-2", "data": "asd", s3store.last_updated_field: datetime.utcnow(), "group": {"level_two": 4}}
]
index_docs = s3store.rebuild_index_from_data(pd.DataFrame(data))
assert len(index_docs) == 1
assert len(s3store.index.index_data) == 1
for key in index_docs.columns:
assert key == "task_id" or key == "last_updated" or key == "group_level_two"
def test_count_subdir(s3store_w_subdir):
s3store_w_subdir.update(
pd.DataFrame(
[{"task_id": "mp-1", "data": {"foo": "asd"}, s3store_w_subdir.last_updated_field: datetime.utcnow()}]
)
)
s3store_w_subdir.update(
pd.DataFrame(
[{"task_id": "mp-2", "data": {"foo": "asd"}, s3store_w_subdir.last_updated_field: datetime.utcnow()}]
)
)
assert len(s3store_w_subdir.query()) == 3
assert len(s3store_w_subdir.query(criteria=None)) == 3
assert s3store_w_subdir.count() == 3
assert s3store_w_subdir.count({"query": "task_id == 'mp-2'"}) == 1
def test_subdir_storage(s3store_w_subdir):
def objects_in_bucket(key):
objs = s3store_w_subdir.s3_client.list_objects_v2(Bucket=s3store_w_subdir.bucket, Prefix=key)
return key in [o["Key"] for o in objs["Contents"]]
s3store_w_subdir.update(
pd.DataFrame(
[{"task_id": "mp-1", "data": {"foo": "asd"}, s3store_w_subdir.last_updated_field: datetime.utcnow()}]
)
)
s3store_w_subdir.update(
pd.DataFrame(
[{"task_id": "mp-2", "data": {"foo": "asd"}, s3store_w_subdir.last_updated_field: datetime.utcnow()}]
)
)
assert objects_in_bucket("subdir1/data_foo=asd.jsonl.gz")
assert objects_in_bucket("subdir1/data_foo=sdf.jsonl.gz")
def test_additional_metadata(s3store):
tic = datetime(2018, 4, 12, 16)
data = [{"task_id": f"mp-{i}", "a": i, s3store.last_updated_field: tic} for i in range(4)]
with pytest.raises(TypeError):
s3store.update(data, key="a", additional_metadata="task_id")
def test_rebuild_index_from_s3_for_tasks_store():
data = [{"task_id": "mp-2", "data": "asd", "last_updated": datetime.utcnow(), "group": {"level_two": 4}}]
with mock_aws():
conn = boto3.resource("s3", region_name="us-east-1")
conn.create_bucket(Bucket="bucket1")
string_io = StringIO()
with jsonlines.Writer(string_io, dumps=json_util.dumps) as writer:
for _, row in pd.DataFrame(data).iterrows():
writer.write(row.to_dict())
client = boto3.client("s3", region_name="us-east-1")
client.put_object(
Bucket="bucket1",
Body=BytesIO(gzip.compress(string_io.getvalue().encode("utf-8"))),
Key="group_level_two=4/dt=some_random_data.jsonl.gz",
)
store = TasksOpenDataStore(
collection_name="index", bucket="bucket1", key="task_id", object_grouping=["group_level_two", "dt"]
)
store.connect()
index_docs = store.rebuild_index_from_s3_data()
assert len(index_docs) == 1
assert len(store.index.index_data) == 1
for key in index_docs.columns:
assert key == "task_id" or key == "last_updated" or key == "group_level_two" or key == "dt"
assert index_docs["dt"].iloc[0] == "some_random_data"
def test_no_update_for_tasks_store():
with mock_aws():
conn = boto3.resource("s3", region_name="us-east-1")
conn.create_bucket(Bucket="bucket1")
store = TasksOpenDataStore(
collection_name="index", bucket="bucket1", key="task_id", object_grouping=["group_level_two", "dt"]
)
store.connect()
with pytest.raises(NotImplementedError):
store.update(
pd.DataFrame(
[
{
"task_id": "mp-199999",
"data": "foo",
"group": {"level_two": 4},
store.last_updated_field: datetime.utcnow(),
}
]
)
)
|