-
Notifications
You must be signed in to change notification settings - Fork 309
/
Copy path_pandas_helpers.py
796 lines (654 loc) · 27.2 KB
/
_pandas_helpers.py
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
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
# Copyright 2019 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Shared helper functions for connecting BigQuery and pandas."""
import concurrent.futures
import functools
import logging
import queue
import warnings
from packaging import version
try:
import pandas
except ImportError: # pragma: NO COVER
pandas = None
try:
import pyarrow
import pyarrow.parquet
except ImportError: # pragma: NO COVER
pyarrow = None
try:
from google.cloud.bigquery_storage import ArrowSerializationOptions
except ImportError:
_ARROW_COMPRESSION_SUPPORT = False
else:
# Having BQ Storage available implies that pyarrow >=1.0.0 is available, too.
_ARROW_COMPRESSION_SUPPORT = True
from google.cloud.bigquery import _helpers
from google.cloud.bigquery import schema
_LOGGER = logging.getLogger(__name__)
_NO_BQSTORAGE_ERROR = (
"The google-cloud-bigquery-storage library is not installed, "
"please install google-cloud-bigquery-storage to use bqstorage features."
)
_PROGRESS_INTERVAL = 0.2 # Maximum time between download status checks, in seconds.
_MAX_QUEUE_SIZE_DEFAULT = object() # max queue size sentinel for BQ Storage downloads
_PANDAS_DTYPE_TO_BQ = {
"bool": "BOOLEAN",
"datetime64[ns, UTC]": "TIMESTAMP",
# BigQuery does not support uploading DATETIME values from Parquet files.
# See: https://github.com/googleapis/google-cloud-python/issues/9996
"datetime64[ns]": "TIMESTAMP",
"float32": "FLOAT",
"float64": "FLOAT",
"int8": "INTEGER",
"int16": "INTEGER",
"int32": "INTEGER",
"int64": "INTEGER",
"uint8": "INTEGER",
"uint16": "INTEGER",
"uint32": "INTEGER",
}
class _DownloadState(object):
"""Flag to indicate that a thread should exit early."""
def __init__(self):
# No need for a lock because reading/replacing a variable is defined to
# be an atomic operation in the Python language definition (enforced by
# the global interpreter lock).
self.done = False
def pyarrow_datetime():
return pyarrow.timestamp("us", tz=None)
def pyarrow_numeric():
return pyarrow.decimal128(38, 9)
def pyarrow_bignumeric():
# 77th digit is partial.
# https://cloud.google.com/bigquery/docs/reference/standard-sql/data-types#decimal_types
return pyarrow.decimal256(76, 38)
def pyarrow_time():
return pyarrow.time64("us")
def pyarrow_timestamp():
return pyarrow.timestamp("us", tz="UTC")
if pyarrow:
# This dictionary is duplicated in bigquery_storage/test/unite/test_reader.py
# When modifying it be sure to update it there as well.
BQ_TO_ARROW_SCALARS = {
"BOOL": pyarrow.bool_,
"BOOLEAN": pyarrow.bool_,
"BYTES": pyarrow.binary,
"DATE": pyarrow.date32,
"DATETIME": pyarrow_datetime,
"FLOAT": pyarrow.float64,
"FLOAT64": pyarrow.float64,
"GEOGRAPHY": pyarrow.string,
"INT64": pyarrow.int64,
"INTEGER": pyarrow.int64,
"NUMERIC": pyarrow_numeric,
"STRING": pyarrow.string,
"TIME": pyarrow_time,
"TIMESTAMP": pyarrow_timestamp,
}
ARROW_SCALAR_IDS_TO_BQ = {
# https://arrow.apache.org/docs/python/api/datatypes.html#type-classes
pyarrow.bool_().id: "BOOL",
pyarrow.int8().id: "INT64",
pyarrow.int16().id: "INT64",
pyarrow.int32().id: "INT64",
pyarrow.int64().id: "INT64",
pyarrow.uint8().id: "INT64",
pyarrow.uint16().id: "INT64",
pyarrow.uint32().id: "INT64",
pyarrow.uint64().id: "INT64",
pyarrow.float16().id: "FLOAT64",
pyarrow.float32().id: "FLOAT64",
pyarrow.float64().id: "FLOAT64",
pyarrow.time32("ms").id: "TIME",
pyarrow.time64("ns").id: "TIME",
pyarrow.timestamp("ns").id: "TIMESTAMP",
pyarrow.date32().id: "DATE",
pyarrow.date64().id: "DATETIME", # because millisecond resolution
pyarrow.binary().id: "BYTES",
pyarrow.string().id: "STRING", # also alias for pyarrow.utf8()
# The exact scale and precision don't matter, see below.
pyarrow.decimal128(38, scale=9).id: "NUMERIC",
}
if version.parse(pyarrow.__version__) >= version.parse("3.0.0"):
BQ_TO_ARROW_SCALARS["BIGNUMERIC"] = pyarrow_bignumeric
# The exact decimal's scale and precision are not important, as only
# the type ID matters, and it's the same for all decimal256 instances.
ARROW_SCALAR_IDS_TO_BQ[pyarrow.decimal256(76, scale=38).id] = "BIGNUMERIC"
_BIGNUMERIC_SUPPORT = True
else:
_BIGNUMERIC_SUPPORT = False
else: # pragma: NO COVER
BQ_TO_ARROW_SCALARS = {} # pragma: NO COVER
ARROW_SCALAR_IDS_TO_BQ = {} # pragma: NO_COVER
_BIGNUMERIC_SUPPORT = False # pragma: NO COVER
def bq_to_arrow_struct_data_type(field):
arrow_fields = []
for subfield in field.fields:
arrow_subfield = bq_to_arrow_field(subfield)
if arrow_subfield:
arrow_fields.append(arrow_subfield)
else:
# Could not determine a subfield type. Fallback to type
# inference.
return None
return pyarrow.struct(arrow_fields)
def bq_to_arrow_data_type(field):
"""Return the Arrow data type, corresponding to a given BigQuery column.
Returns:
None: if default Arrow type inspection should be used.
"""
if field.mode is not None and field.mode.upper() == "REPEATED":
inner_type = bq_to_arrow_data_type(
schema.SchemaField(field.name, field.field_type, fields=field.fields)
)
if inner_type:
return pyarrow.list_(inner_type)
return None
field_type_upper = field.field_type.upper() if field.field_type else ""
if field_type_upper in schema._STRUCT_TYPES:
return bq_to_arrow_struct_data_type(field)
data_type_constructor = BQ_TO_ARROW_SCALARS.get(field_type_upper)
if data_type_constructor is None:
return None
return data_type_constructor()
def bq_to_arrow_field(bq_field):
"""Return the Arrow field, corresponding to a given BigQuery column.
Returns:
None: if the Arrow type cannot be determined.
"""
arrow_type = bq_to_arrow_data_type(bq_field)
if arrow_type:
is_nullable = bq_field.mode.upper() == "NULLABLE"
return pyarrow.field(bq_field.name, arrow_type, nullable=is_nullable)
warnings.warn("Unable to determine type for field '{}'.".format(bq_field.name))
return None
def bq_to_arrow_schema(bq_schema):
"""Return the Arrow schema, corresponding to a given BigQuery schema.
Returns:
None: if any Arrow type cannot be determined.
"""
arrow_fields = []
for bq_field in bq_schema:
arrow_field = bq_to_arrow_field(bq_field)
if arrow_field is None:
# Auto-detect the schema if there is an unknown field type.
return None
arrow_fields.append(arrow_field)
return pyarrow.schema(arrow_fields)
def bq_to_arrow_array(series, bq_field):
arrow_type = bq_to_arrow_data_type(bq_field)
field_type_upper = bq_field.field_type.upper() if bq_field.field_type else ""
if bq_field.mode.upper() == "REPEATED":
return pyarrow.ListArray.from_pandas(series, type=arrow_type)
if field_type_upper in schema._STRUCT_TYPES:
return pyarrow.StructArray.from_pandas(series, type=arrow_type)
return pyarrow.Array.from_pandas(series, type=arrow_type)
def get_column_or_index(dataframe, name):
"""Return a column or index as a pandas series."""
if name in dataframe.columns:
return dataframe[name].reset_index(drop=True)
if isinstance(dataframe.index, pandas.MultiIndex):
if name in dataframe.index.names:
return (
dataframe.index.get_level_values(name)
.to_series()
.reset_index(drop=True)
)
else:
if name == dataframe.index.name:
return dataframe.index.to_series().reset_index(drop=True)
raise ValueError("column or index '{}' not found.".format(name))
def list_columns_and_indexes(dataframe):
"""Return all index and column names with dtypes.
Returns:
Sequence[Tuple[str, dtype]]:
Returns a sorted list of indexes and column names with
corresponding dtypes. If an index is missing a name or has the
same name as a column, the index is omitted.
"""
column_names = frozenset(dataframe.columns)
columns_and_indexes = []
if isinstance(dataframe.index, pandas.MultiIndex):
for name in dataframe.index.names:
if name and name not in column_names:
values = dataframe.index.get_level_values(name)
columns_and_indexes.append((name, values.dtype))
else:
if dataframe.index.name and dataframe.index.name not in column_names:
columns_and_indexes.append((dataframe.index.name, dataframe.index.dtype))
columns_and_indexes += zip(dataframe.columns, dataframe.dtypes)
return columns_and_indexes
def dataframe_to_bq_schema(dataframe, bq_schema):
"""Convert a pandas DataFrame schema to a BigQuery schema.
Args:
dataframe (pandas.DataFrame):
DataFrame for which the client determines the BigQuery schema.
bq_schema (Sequence[Union[ \
:class:`~google.cloud.bigquery.schema.SchemaField`, \
Mapping[str, Any] \
]]):
A BigQuery schema. Use this argument to override the autodetected
type for some or all of the DataFrame columns.
Returns:
Optional[Sequence[google.cloud.bigquery.schema.SchemaField]]:
The automatically determined schema. Returns None if the type of
any column cannot be determined.
"""
if bq_schema:
bq_schema = schema._to_schema_fields(bq_schema)
bq_schema_index = {field.name: field for field in bq_schema}
bq_schema_unused = set(bq_schema_index.keys())
else:
bq_schema_index = {}
bq_schema_unused = set()
bq_schema_out = []
unknown_type_fields = []
for column, dtype in list_columns_and_indexes(dataframe):
# Use provided type from schema, if present.
bq_field = bq_schema_index.get(column)
if bq_field:
bq_schema_out.append(bq_field)
bq_schema_unused.discard(bq_field.name)
continue
# Otherwise, try to automatically determine the type based on the
# pandas dtype.
bq_type = _PANDAS_DTYPE_TO_BQ.get(dtype.name)
bq_field = schema.SchemaField(column, bq_type)
bq_schema_out.append(bq_field)
if bq_field.field_type is None:
unknown_type_fields.append(bq_field)
# Catch any schema mismatch. The developer explicitly asked to serialize a
# column, but it was not found.
if bq_schema_unused:
raise ValueError(
u"bq_schema contains fields not present in dataframe: {}".format(
bq_schema_unused
)
)
# If schema detection was not successful for all columns, also try with
# pyarrow, if available.
if unknown_type_fields:
if not pyarrow:
msg = u"Could not determine the type of columns: {}".format(
", ".join(field.name for field in unknown_type_fields)
)
warnings.warn(msg)
return None # We cannot detect the schema in full.
# The augment_schema() helper itself will also issue unknown type
# warnings if detection still fails for any of the fields.
bq_schema_out = augment_schema(dataframe, bq_schema_out)
return tuple(bq_schema_out) if bq_schema_out else None
def augment_schema(dataframe, current_bq_schema):
"""Try to deduce the unknown field types and return an improved schema.
This function requires ``pyarrow`` to run. If all the missing types still
cannot be detected, ``None`` is returned. If all types are already known,
a shallow copy of the given schema is returned.
Args:
dataframe (pandas.DataFrame):
DataFrame for which some of the field types are still unknown.
current_bq_schema (Sequence[google.cloud.bigquery.schema.SchemaField]):
A BigQuery schema for ``dataframe``. The types of some or all of
the fields may be ``None``.
Returns:
Optional[Sequence[google.cloud.bigquery.schema.SchemaField]]
"""
# pytype: disable=attribute-error
augmented_schema = []
unknown_type_fields = []
for field in current_bq_schema:
if field.field_type is not None:
augmented_schema.append(field)
continue
arrow_table = pyarrow.array(dataframe[field.name])
detected_type = ARROW_SCALAR_IDS_TO_BQ.get(arrow_table.type.id)
if detected_type is None:
unknown_type_fields.append(field)
continue
new_field = schema.SchemaField(
name=field.name,
field_type=detected_type,
mode=field.mode,
description=field.description,
fields=field.fields,
)
augmented_schema.append(new_field)
if unknown_type_fields:
warnings.warn(
u"Pyarrow could not determine the type of columns: {}.".format(
", ".join(field.name for field in unknown_type_fields)
)
)
return None
return augmented_schema
# pytype: enable=attribute-error
def dataframe_to_arrow(dataframe, bq_schema):
"""Convert pandas dataframe to Arrow table, using BigQuery schema.
Args:
dataframe (pandas.DataFrame):
DataFrame to convert to Arrow table.
bq_schema (Sequence[Union[ \
:class:`~google.cloud.bigquery.schema.SchemaField`, \
Mapping[str, Any] \
]]):
Desired BigQuery schema. The number of columns must match the
number of columns in the DataFrame.
Returns:
pyarrow.Table:
Table containing dataframe data, with schema derived from
BigQuery schema.
"""
column_names = set(dataframe.columns)
column_and_index_names = set(
name for name, _ in list_columns_and_indexes(dataframe)
)
bq_schema = schema._to_schema_fields(bq_schema)
bq_field_names = set(field.name for field in bq_schema)
extra_fields = bq_field_names - column_and_index_names
if extra_fields:
raise ValueError(
u"bq_schema contains fields not present in dataframe: {}".format(
extra_fields
)
)
# It's okay for indexes to be missing from bq_schema, but it's not okay to
# be missing columns.
missing_fields = column_names - bq_field_names
if missing_fields:
raise ValueError(
u"bq_schema is missing fields from dataframe: {}".format(missing_fields)
)
arrow_arrays = []
arrow_names = []
arrow_fields = []
for bq_field in bq_schema:
arrow_fields.append(bq_to_arrow_field(bq_field))
arrow_names.append(bq_field.name)
arrow_arrays.append(
bq_to_arrow_array(get_column_or_index(dataframe, bq_field.name), bq_field)
)
if all((field is not None for field in arrow_fields)):
return pyarrow.Table.from_arrays(
arrow_arrays, schema=pyarrow.schema(arrow_fields)
)
return pyarrow.Table.from_arrays(arrow_arrays, names=arrow_names)
def dataframe_to_parquet(dataframe, bq_schema, filepath, parquet_compression="SNAPPY"):
"""Write dataframe as a Parquet file, according to the desired BQ schema.
This function requires the :mod:`pyarrow` package. Arrow is used as an
intermediate format.
Args:
dataframe (pandas.DataFrame):
DataFrame to convert to Parquet file.
bq_schema (Sequence[Union[ \
:class:`~google.cloud.bigquery.schema.SchemaField`, \
Mapping[str, Any] \
]]):
Desired BigQuery schema. Number of columns must match number of
columns in the DataFrame.
filepath (str):
Path to write Parquet file to.
parquet_compression (Optional[str]):
The compression codec to use by the the ``pyarrow.parquet.write_table``
serializing method. Defaults to "SNAPPY".
https://arrow.apache.org/docs/python/generated/pyarrow.parquet.write_table.html#pyarrow-parquet-write-table
"""
if pyarrow is None:
raise ValueError("pyarrow is required for BigQuery schema conversion.")
bq_schema = schema._to_schema_fields(bq_schema)
arrow_table = dataframe_to_arrow(dataframe, bq_schema)
pyarrow.parquet.write_table(arrow_table, filepath, compression=parquet_compression)
def _row_iterator_page_to_arrow(page, column_names, arrow_types):
# Iterate over the page to force the API request to get the page data.
try:
next(iter(page))
except StopIteration:
pass
arrays = []
for column_index, arrow_type in enumerate(arrow_types):
arrays.append(pyarrow.array(page._columns[column_index], type=arrow_type))
if isinstance(column_names, pyarrow.Schema):
return pyarrow.RecordBatch.from_arrays(arrays, schema=column_names)
return pyarrow.RecordBatch.from_arrays(arrays, names=column_names)
def download_arrow_row_iterator(pages, bq_schema):
"""Use HTTP JSON RowIterator to construct an iterable of RecordBatches.
Args:
pages (Iterator[:class:`google.api_core.page_iterator.Page`]):
An iterator over the result pages.
bq_schema (Sequence[Union[ \
:class:`~google.cloud.bigquery.schema.SchemaField`, \
Mapping[str, Any] \
]]):
A decription of the fields in result pages.
Yields:
:class:`pyarrow.RecordBatch`
The next page of records as a ``pyarrow`` record batch.
"""
bq_schema = schema._to_schema_fields(bq_schema)
column_names = bq_to_arrow_schema(bq_schema) or [field.name for field in bq_schema]
arrow_types = [bq_to_arrow_data_type(field) for field in bq_schema]
for page in pages:
yield _row_iterator_page_to_arrow(page, column_names, arrow_types)
def _row_iterator_page_to_dataframe(page, column_names, dtypes):
# Iterate over the page to force the API request to get the page data.
try:
next(iter(page))
except StopIteration:
pass
columns = {}
for column_index, column_name in enumerate(column_names):
dtype = dtypes.get(column_name)
columns[column_name] = pandas.Series(page._columns[column_index], dtype=dtype)
return pandas.DataFrame(columns, columns=column_names)
def download_dataframe_row_iterator(pages, bq_schema, dtypes):
"""Use HTTP JSON RowIterator to construct a DataFrame.
Args:
pages (Iterator[:class:`google.api_core.page_iterator.Page`]):
An iterator over the result pages.
bq_schema (Sequence[Union[ \
:class:`~google.cloud.bigquery.schema.SchemaField`, \
Mapping[str, Any] \
]]):
A decription of the fields in result pages.
dtypes(Mapping[str, numpy.dtype]):
The types of columns in result data to hint construction of the
resulting DataFrame. Not all column types have to be specified.
Yields:
:class:`pandas.DataFrame`
The next page of records as a ``pandas.DataFrame`` record batch.
"""
bq_schema = schema._to_schema_fields(bq_schema)
column_names = [field.name for field in bq_schema]
for page in pages:
yield _row_iterator_page_to_dataframe(page, column_names, dtypes)
def _bqstorage_page_to_arrow(page):
return page.to_arrow()
def _bqstorage_page_to_dataframe(column_names, dtypes, page):
# page.to_dataframe() does not preserve column order in some versions
# of google-cloud-bigquery-storage. Access by column name to rearrange.
return page.to_dataframe(dtypes=dtypes)[column_names]
def _download_table_bqstorage_stream(
download_state, bqstorage_client, session, stream, worker_queue, page_to_item
):
reader = bqstorage_client.read_rows(stream.name)
# Avoid deprecation warnings for passing in unnecessary read session.
# https://github.com/googleapis/python-bigquery-storage/issues/229
if _helpers.BQ_STORAGE_VERSIONS.is_read_session_optional:
rowstream = reader.rows()
else:
rowstream = reader.rows(session)
for page in rowstream.pages:
if download_state.done:
return
item = page_to_item(page)
worker_queue.put(item)
def _nowait(futures):
"""Separate finished and unfinished threads, much like
:func:`concurrent.futures.wait`, but don't wait.
"""
done = []
not_done = []
for future in futures:
if future.done():
done.append(future)
else:
not_done.append(future)
return done, not_done
def _download_table_bqstorage(
project_id,
table,
bqstorage_client,
preserve_order=False,
selected_fields=None,
page_to_item=None,
max_queue_size=_MAX_QUEUE_SIZE_DEFAULT,
):
"""Use (faster, but billable) BQ Storage API to construct DataFrame."""
# Passing a BQ Storage client in implies that the BigQuery Storage library
# is available and can be imported.
from google.cloud import bigquery_storage
if "$" in table.table_id:
raise ValueError(
"Reading from a specific partition is not currently supported."
)
if "@" in table.table_id:
raise ValueError("Reading from a specific snapshot is not currently supported.")
requested_streams = 1 if preserve_order else 0
requested_session = bigquery_storage.types.ReadSession(
table=table.to_bqstorage(), data_format=bigquery_storage.types.DataFormat.ARROW
)
if selected_fields is not None:
for field in selected_fields:
requested_session.read_options.selected_fields.append(field.name)
if _ARROW_COMPRESSION_SUPPORT:
requested_session.read_options.arrow_serialization_options.buffer_compression = (
ArrowSerializationOptions.CompressionCodec.LZ4_FRAME
)
session = bqstorage_client.create_read_session(
parent="projects/{}".format(project_id),
read_session=requested_session,
max_stream_count=requested_streams,
)
_LOGGER.debug(
"Started reading table '{}.{}.{}' with BQ Storage API session '{}'.".format(
table.project, table.dataset_id, table.table_id, session.name
)
)
# Avoid reading rows from an empty table.
if not session.streams:
return
total_streams = len(session.streams)
# Use _DownloadState to notify worker threads when to quit.
# See: https://stackoverflow.com/a/29237343/101923
download_state = _DownloadState()
# Create a queue to collect frames as they are created in each thread.
#
# The queue needs to be bounded by default, because if the user code processes the
# fetched result pages too slowly, while at the same time new pages are rapidly being
# fetched from the server, the queue can grow to the point where the process runs
# out of memory.
if max_queue_size is _MAX_QUEUE_SIZE_DEFAULT:
max_queue_size = total_streams
elif max_queue_size is None:
max_queue_size = 0 # unbounded
worker_queue = queue.Queue(maxsize=max_queue_size)
with concurrent.futures.ThreadPoolExecutor(max_workers=total_streams) as pool:
try:
# Manually submit jobs and wait for download to complete rather
# than using pool.map because pool.map continues running in the
# background even if there is an exception on the main thread.
# See: https://github.com/googleapis/google-cloud-python/pull/7698
not_done = [
pool.submit(
_download_table_bqstorage_stream,
download_state,
bqstorage_client,
session,
stream,
worker_queue,
page_to_item,
)
for stream in session.streams
]
while not_done:
# Don't block on the worker threads. For performance reasons,
# we want to block on the queue's get method, instead. This
# prevents the queue from filling up, because the main thread
# has smaller gaps in time between calls to the queue's get
# method. For a detailed explaination, see:
# https://friendliness.dev/2019/06/18/python-nowait/
done, not_done = _nowait(not_done)
for future in done:
# Call result() on any finished threads to raise any
# exceptions encountered.
future.result()
try:
frame = worker_queue.get(timeout=_PROGRESS_INTERVAL)
yield frame
except queue.Empty: # pragma: NO COVER
continue
# Return any remaining values after the workers finished.
while True: # pragma: NO COVER
try:
frame = worker_queue.get_nowait()
yield frame
except queue.Empty: # pragma: NO COVER
break
finally:
# No need for a lock because reading/replacing a variable is
# defined to be an atomic operation in the Python language
# definition (enforced by the global interpreter lock).
download_state.done = True
# Shutdown all background threads, now that they should know to
# exit early.
pool.shutdown(wait=True)
def download_arrow_bqstorage(
project_id, table, bqstorage_client, preserve_order=False, selected_fields=None,
):
return _download_table_bqstorage(
project_id,
table,
bqstorage_client,
preserve_order=preserve_order,
selected_fields=selected_fields,
page_to_item=_bqstorage_page_to_arrow,
)
def download_dataframe_bqstorage(
project_id,
table,
bqstorage_client,
column_names,
dtypes,
preserve_order=False,
selected_fields=None,
max_queue_size=_MAX_QUEUE_SIZE_DEFAULT,
):
page_to_item = functools.partial(_bqstorage_page_to_dataframe, column_names, dtypes)
return _download_table_bqstorage(
project_id,
table,
bqstorage_client,
preserve_order=preserve_order,
selected_fields=selected_fields,
page_to_item=page_to_item,
max_queue_size=max_queue_size,
)
def dataframe_to_json_generator(dataframe):
for row in dataframe.itertuples(index=False, name=None):
output = {}
for column, value in zip(dataframe.columns, row):
# Omit NaN values.
if pandas.isna(value):
continue
output[column] = value
yield output