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
|
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
import sys
import math
from collections import OrderedDict
from datetime import datetime, date, time
from decimal import Decimal
from petl.compat import izip_longest, text_type, string_types, PY3
from petl.io.sources import read_source_from_arg, write_source_from_arg
from petl.transform.headers import skip, setheader
from petl.util.base import Table, dicts, fieldnames, iterpeek, wrap
# region API
def fromavro(source, limit=None, skips=0, **avro_args):
"""Extract a table from the records of a avro file.
The `source` argument (string or file-like or fastavro.reader) can either
be the path of the file, a file-like input stream or a instance from
fastavro.reader.
The `limit` and `skip` arguments can be used to limit the range of rows
to extract.
The `sample` argument (int, optional) defines how many rows are inspected
for discovering the field types and building a schema for the avro file
when the `schema` argument is not passed.
The rows fields read from file can have scalar values like int, string,
float, datetime, date and decimal but can also have compound types like
enum, :ref:`array <array_schema>`, map, union and record.
The fields types can also have recursive structures defined
in :ref:`complex schemas <complex_schema>`.
Also types with :ref:`logical types <logical_schema>` types are read and
translated to coresponding python types: long timestamp-millis and
long timestamp-micros: datetime.datetime, int date: datetime.date,
bytes decimal and fixed decimal: Decimal, int time-millis and
long time-micros: datetime.time.
Example usage for reading files::
>>> # set up a Avro file to demonstrate with
...
>>> schema1 = {
... 'doc': 'Some people records.',
... 'name': 'People',
... 'namespace': 'test',
... 'type': 'record',
... 'fields': [
... {'name': 'name', 'type': 'string'},
... {'name': 'friends', 'type': 'int'},
... {'name': 'age', 'type': 'int'},
... ]
... }
...
>>> records1 = [
... {'name': 'Bob', 'friends': 42, 'age': 33},
... {'name': 'Jim', 'friends': 13, 'age': 69},
... {'name': 'Joe', 'friends': 86, 'age': 17},
... {'name': 'Ted', 'friends': 23, 'age': 51}
... ]
...
>>> import fastavro
>>> parsed_schema1 = fastavro.parse_schema(schema1)
>>> with open('example.file1.avro', 'wb') as f1:
... fastavro.writer(f1, parsed_schema1, records1)
...
>>> # now demonstrate the use of fromavro()
>>> import petl as etl
>>> tbl1 = etl.fromavro('example.file1.avro')
>>> tbl1
+-------+---------+-----+
| name | friends | age |
+=======+=========+=====+
| 'Bob' | 42 | 33 |
+-------+---------+-----+
| 'Jim' | 13 | 69 |
+-------+---------+-----+
| 'Joe' | 86 | 17 |
+-------+---------+-----+
| 'Ted' | 23 | 51 |
+-------+---------+-----+
.. versionadded:: 1.4.0
"""
source2 = read_source_from_arg(source)
return AvroView(source=source2,
limit=limit,
skips=skips,
**avro_args)
def toavro(table, target, schema=None, sample=9,
codec='deflate', compression_level=None, **avro_args):
"""
Write the table into a new avro file according to schema passed.
This method assume that each column has values with the same type
for all rows of the source `table`.
`Apache Avro`_ is a data
serialization framework. It is used in data serialization (especially in
Hadoop ecosystem), for dataexchange for databases (Redshift) and RPC
protocols (like in Kafka). It has libraries to support many languages and
generally is faster and safer than text formats like Json, XML or CSV.
The `target` argument is the file path for creating the avro file.
Note that if a file already exists at the given location, it will be
overwritten.
The `schema` argument (dict) defines the rows field structure of the file.
Check fastavro `documentation`_ and Avro schema `reference`_ for details.
The `sample` argument (int, optional) defines how many rows are inspected
for discovering the field types and building a schema for the avro file
when the `schema` argument is not passed.
The `codec` argument (string, optional) sets the compression codec used to
shrink data in the file. It can be 'null', 'deflate' (default), 'bzip2' or
'snappy', 'zstandard', 'lz4', 'xz' (if installed)
The `compression_level` argument (int, optional) sets the level of
compression to use with the specified codec (if the codec supports it)
Additionally there are support for passing extra options in the
argument `**avro_args` that are fowarded directly to fastavro. Check the
fastavro `documentation`_ for reference.
The avro file format preserves type information, i.e., reading and writing
is round-trippable for tables with non-string data values. However the
conversion from Python value types to avro fields is not perfect. Use the
`schema` argument to define proper type to the conversion.
The following avro types are supported by the schema: null, boolean,
string, int, long, float, double, bytes, fixed, enum,
:ref:`array <array_schema>`, map, union, record, and recursive types
defined in :ref:`complex schemas <complex_schema>`.
Also :ref:`logical types <logical_schema>` are supported and translated to
coresponding python types: long timestamp-millis, long timestamp-micros, int date,
bytes decimal, fixed decimal, string uuid, int time-millis, long time-micros.
Example usage for writing files::
>>> # set up a Avro file to demonstrate with
>>> table2 = [['name', 'friends', 'age'],
... ['Bob', 42, 33],
... ['Jim', 13, 69],
... ['Joe', 86, 17],
... ['Ted', 23, 51]]
...
>>> schema2 = {
... 'doc': 'Some people records.',
... 'name': 'People',
... 'namespace': 'test',
... 'type': 'record',
... 'fields': [
... {'name': 'name', 'type': 'string'},
... {'name': 'friends', 'type': 'int'},
... {'name': 'age', 'type': 'int'},
... ]
... }
...
>>> # now demonstrate what writing with toavro()
>>> import petl as etl
>>> etl.toavro(table2, 'example.file2.avro', schema=schema2)
...
>>> # this was what was saved above
>>> tbl2 = etl.fromavro('example.file2.avro')
>>> tbl2
+-------+---------+-----+
| name | friends | age |
+=======+=========+=====+
| 'Bob' | 42 | 33 |
+-------+---------+-----+
| 'Jim' | 13 | 69 |
+-------+---------+-----+
| 'Joe' | 86 | 17 |
+-------+---------+-----+
| 'Ted' | 23 | 51 |
+-------+---------+-----+
.. versionadded:: 1.4.0
.. _Apache Avro: https://avro.apache.org/docs/current/spec.html
.. _reference: https://avro.apache.org/docs/current/spec.html#schemas
.. _documentation : https://fastavro.readthedocs.io/en/latest/writer.html
"""
_write_toavro(table,
target=target,
mode='wb',
schema=schema,
sample=sample,
codec=codec,
compression_level=compression_level,
**avro_args)
def appendavro(table, target, schema=None, sample=9, **avro_args):
"""
Append rows into a avro existing avro file or create a new one.
The `target` argument can be either an existing avro file or the file
path for creating new one.
The `schema` argument is checked against the schema of the existing file.
So it must be the same schema as used by `toavro()` or the schema of the
existing file.
The `sample` argument (int, optional) defines how many rows are inspected
for discovering the field types and building a schema for the avro file
when the `schema` argument is not passed.
Additionally there are support for passing extra options in the
argument `**avro_args` that are fowarded directly to fastavro. Check the
fastavro documentation for reference.
See :meth:`petl.io.avro.toavro` method for more information and examples.
.. versionadded:: 1.4.0
"""
_write_toavro(table,
target=target,
mode='a+b',
schema=schema,
sample=sample,
**avro_args)
# endregion API
# region Implementation
class AvroView(Table):
'''Read rows from avro file with their types and logical types'''
def __init__(self, source, limit, skips, **avro_args):
self.source = source
self.limit = limit
self.skip = skips
self.avro_args = avro_args
self.avro_schema = None
def get_avro_schema(self):
'''gets the schema stored in avro file header'''
return self.avro_schema
def __iter__(self):
with self.source.open('rb') as source_file:
avro_reader = self._open_reader(source_file)
header = self._decode_schema(avro_reader)
yield header
for row in self._read_rows_from(avro_reader, header):
yield row
def _open_reader(self, source_file):
'''This could raise a error when the file is corrupt or is not avro'''
# delay the import of fastavro for not breaking when unused
import fastavro
avro_reader = fastavro.reader(source_file, **self.avro_args)
return avro_reader
def _decode_schema(self, avro_reader):
'''extract the header from schema stored in avro file header'''
self.avro_schema = avro_reader.writer_schema
if self.avro_schema is None:
return None, None
schema_fields = self.avro_schema['fields']
header = tuple(col['name'] for col in schema_fields)
return header
def _read_rows_from(self, avro_reader, header):
count = 0
maximum = self.limit if self.limit is not None else sys.maxsize
for i, record in enumerate(avro_reader):
if i < self.skip:
continue
if count >= maximum:
break
count += 1
row = self._map_row_from(header, record)
yield row
def _map_row_from(self, header, record):
'''
fastavro auto converts logical types defined in avro schema to
correspoding python types. E.g:
- avro type: long logicalType: timestamp-millis -> python datetime
- avro type: int logicalType: date -> python date
- avro type: bytes logicalType: decimal -> python Decimal
'''
if header is None or PY3:
r = tuple(record.values())
else:
# fastavro on python2 does not respect dict order
r = tuple(record.get(col) for col in header)
return r
def _write_toavro(table, target, mode, schema, sample,
codec='deflate', compression_level=None, **avro_args):
if table is None:
return
# build a schema when not defined by user
if not schema:
schema, table2 = _build_schema_from_values(table, sample)
else:
table2 = _fix_missing_headers(table, schema)
# fastavro expects a iterator of dicts
rows = dicts(table2) if PY3 else _ordered_dict_iterator(table2)
target2 = write_source_from_arg(target, mode=mode)
with target2.open(mode) as target_file:
# delay the import of fastavro for not breaking when unused
from fastavro import parse_schema
from fastavro.write import Writer
parsed_schema = parse_schema(schema)
writer = Writer(fo=target_file,
schema=parsed_schema,
codec=codec,
compression_level=compression_level,
**avro_args)
num = 1
for record in rows:
try:
writer.write(record)
num = num + 1
except ValueError as verr:
vmsg = _get_error_details(target, num, verr, record, schema)
_raise_error(ValueError, vmsg)
except TypeError as terr:
tmsg = _get_error_details(target, num, terr, record, schema)
_raise_error(TypeError, tmsg)
# finish writing
writer.flush()
# endregion Implementation
# region Helpers
def _build_schema_from_values(table, sample):
# table2: try not advance iterators
samples, table2 = iterpeek(table, sample + 1)
props = fieldnames(samples)
peek = skip(samples, 1)
schema_fields = _build_schema_fields_from_values(peek, props)
schema_source = _build_schema_with(schema_fields)
return schema_source, table2
def _build_schema_with(schema_fields):
schema = {
'type': 'record',
'name': 'output',
'namespace': 'avro',
'doc': 'generated by petl',
'fields': schema_fields,
}
return schema
def _build_schema_fields_from_values(peek, props):
# store the previous for calculate max precision and max scale
previous = OrderedDict()
# set a default when value is None in the first row but allow override after
fill_missing = True
fields = OrderedDict()
# iterate on sample rows for dealing with columns with None values
for row in peek:
_update_field_defs_from(props, row, fields, previous, fill_missing)
fill_missing = False
schema_fields = [item for item in fields.values()]
return schema_fields
def _update_field_defs_from(props, row, fields, previous, fill_missing):
for prop, val in izip_longest(props, row):
if prop is None:
break
dprev = previous.get(prop + '_prec')
fprev = previous.get(prop + '_prop')
fcurr = None
if isinstance(val, dict):
# get the fields from a recursive definition of record inside this field
tdef, dcurr, fcurr = _get_definition_from_record(prop, val, fprev, dprev, fill_missing)
else:
# get the field definition for building the schema
tdef, dcurr = _get_definition_from_type_of(prop, val, dprev)
if tdef is not None:
fields[prop] = {'name': prop, 'type': ['null', tdef]}
elif fill_missing:
fields[prop] = {'name': prop, 'type': ['null', 'string']}
if dcurr is not None:
previous[prop + '_prec'] = dcurr
if fcurr is not None:
previous[prop + '_prop'] = fcurr
def _get_definition_from_type_of(prop, val, prev):
# TODO: get type for enum, map and other python types
tdef = None
curr = None
if isinstance(val, datetime):
tdef = {'type': 'long', 'logicalType': 'timestamp-millis'}
elif isinstance(val, time):
tdef = {'type': 'int', 'logicalType': 'time-millis'}
elif isinstance(val, date):
tdef = {'type': 'int', 'logicalType': 'date'}
elif isinstance(val, Decimal):
curr, precision, scale = _get_precision_from_decimal(curr, val, prev)
tdef = {'type': 'bytes', 'logicalType': 'decimal',
'precision': precision, 'scale': scale, }
elif isinstance(val, bytes):
tdef = 'bytes'
elif isinstance(val, list):
tdef, curr = _get_definition_from_array(prop, val, prev)
elif isinstance(val, bool):
tdef = 'boolean'
elif isinstance(val, float):
tdef = 'double'
elif isinstance(val, int):
tdef = 'long'
elif val is not None:
tdef = 'string'
else:
return None, None
return tdef, curr
def _get_definition_from_array(prop, val, prev):
afield = None
for item in iter(val):
if item is None:
continue
field2, curr2 = _get_definition_from_type_of(prop, item, prev)
if field2 is not None:
afield = field2
if curr2 is not None:
prev = curr2
bfield = 'string' if afield is None else afield
tdef = {'type': 'array', 'items': bfield}
return tdef, prev
def _get_definition_from_record(prop, val, fprev, dprev, fill_missing):
if fprev is None:
fprev = OrderedDict()
if dprev is None:
dprev = OrderedDict()
props = list(val.keys())
row = list(val.values())
_update_field_defs_from(props, row, fprev, dprev, fill_missing)
schema_fields = [item for item in fprev.values()]
tdef = {
'type': 'record',
'name': prop + '_record',
'namespace': 'avro',
'fields': schema_fields,
}
return tdef, dprev, fprev
def _get_precision_from_decimal(curr, val, prev):
if val is None:
prec = scale = 0
else:
prec, scale, _, _ = precision_and_scale(val)
if prev is not None:
# get the greatests precision and scale of the sample
prec0, scale0 = prev.get('precision'), prev.get('scale')
prec, scale = max(prec, prec0), max(scale, scale0)
prec = max(prec, 8)
curr = {'precision': prec, 'scale': scale, }
return curr, prec, scale
def precision_and_scale(numeric_value):
sign, digits, exp = numeric_value.as_tuple()
number = 0
for digit in digits:
number = (number * 10) + digit
# delta = exp + scale
delta = 1
number = 10 ** delta * number
inumber = int(number)
bits_req = inumber.bit_length() + 1
bytes_req = (bits_req + 8) // 8
if sign:
inumber = - inumber
prec = int(math.ceil(math.log10(abs(inumber))))
scale = abs(exp)
return prec, scale, bytes_req, inumber
def _fix_missing_headers(table, schema):
'''add missing columns headers from schema'''
if schema is None or 'fields' not in schema:
return table
# table2: try not advance iterators
sample, table2 = iterpeek(table, 2)
cols = fieldnames(sample)
headers = _get_schema_header_names(schema)
if len(cols) >= len(headers):
return table2
table3 = setheader(table2, headers)
return table3
def _get_error_details(target, num, err, record, schema):
'''show last row when failed writing for throubleshooting'''
headers = _get_schema_header_names(schema)
if isinstance(record, dict):
table = [headers, list(record.values())]
else:
table = [headers, record]
example = wrap(table).look()
dest = " output: %s" % target if isinstance(target, string_types) else ''
printed = "failed writing on row #%d: %s\n%s\n schema: %s\n%s"
details = printed % (num, err, dest, schema, example)
return details
def _get_schema_header_names(schema):
fields = schema.get('fields')
if fields is None:
return []
header = [field.get('name') for field in fields]
return header
def _raise_error(ErrorType, new_message):
"""Works like raise Excetion(msg) from prev_exp in python3."""
exinf = sys.exc_info()
tracebk = exinf[2]
try:
if PY3:
raise ErrorType(new_message).with_traceback(tracebk)
# Python2 compatibility workaround
exec('raise ErrorType, new_message, tracebk')
finally:
exinf = None
tracebk = None # noqa: F841
def _ordered_dict_iterator(table):
it = iter(table)
hdr = next(it)
flds = [text_type(f) for f in hdr]
for row in it:
items = list()
for i, f in enumerate(flds):
try:
v = row[i]
except IndexError:
v = None
items.append((f, v))
yield OrderedDict(items)
Table.toavro = toavro
Table.appendavro = appendavro
# endregion
|