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Compressed output format (jsongz) for rethinkdb export/import #251

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Compressed output format (jsongz) for rethinkdb export/import #251

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5ec52e0
feat: jsongz export/import
iantocristian Jan 24, 2021
f6e3e40
chore: pylintify
iantocristian Feb 19, 2021
a6d8978
fix: allow single file jsongz import
iantocristian Mar 22, 2021
a88f11c
fix: apply --max-document-size for directory imports too
iantocristian Mar 22, 2021
1e61100
fix: allow compression_level -1
iantocristian Mar 26, 2021
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77 changes: 74 additions & 3 deletions rethinkdb/_export.py
100755 → 100644
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
import tempfile
import time
import traceback
import zlib
from multiprocessing.queues import SimpleQueue

import six
Expand All @@ -48,7 +49,7 @@

usage = """rethinkdb export [-c HOST:PORT] [-p] [--password-file FILENAME] [--tls-cert filename] [-d DIR]
[-e (DB | DB.TABLE)]...
[--format (csv | json | ndjson)] [--fields FIELD,FIELD...] [--delimiter CHARACTER]
[--format (csv | json | ndjson | jsongz)] [--fields FIELD,FIELD...] [--delimiter CHARACTER]
[--clients NUM]"""
help_description = (
"`rethinkdb export` exports data from a RethinkDB cluster into a directory"
Expand Down Expand Up @@ -118,11 +119,11 @@ def parse_options(argv, prog=None):
parser.add_option(
"--format",
dest="format",
metavar="json|csv|ndjson",
metavar="json|csv|ndjson|jsongz",
default="json",
help="format to write (defaults to json. ndjson is newline delimited json.)",
type="choice",
choices=["json", "csv", "ndjson"],
choices=["json", "csv", "ndjson", "jsongz"],
)
parser.add_option(
"--clients",
Expand Down Expand Up @@ -150,6 +151,17 @@ def parse_options(argv, prog=None):
)
parser.add_option_group(csvGroup)

jsongzGroup = optparse.OptionGroup(parser, "jsongz options")
jsongzGroup.add_option(
"--compression-level",
dest="compression_level",
metavar="NUM",
default=None,
help="compression level, an integer from 0 to 9 (defaults to -1 default zlib compression)",
type="int",
)
parser.add_option_group(jsongzGroup)

options, args = parser.parse_args(argv)

# -- Check validity of arguments
Expand Down Expand Up @@ -185,6 +197,15 @@ def parse_options(argv, prog=None):
if options.delimiter:
parser.error("--delimiter option is only valid for CSV file formats")

if options.format == "jsongz":
if options.compression_level is None:
options.compression_level = -1
elif options.compression_level < 0 or options.compression_level > 9:
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What if someone passes -1 as option?
In my opinion it should be changed into elif options.compression_level < -1 or options.compression_level > 9:

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@iantocristian iantocristian Mar 24, 2021 •
edited
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My reasoning was: passing -1 is the same as not specifying the compression level, it's not really setting the compression_level.
Happy to make the change as suggested though, it might make it easier to switch between setting and not setting the compression level.

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I understand your reasoning, but then if someone passes -1, if options.compression_level is None is evaluated False, if options.compression_level < 0 or options.compression_level > 9 is evaluated to True and raises an exception. Which is incorrect, since -1 is an acceptable value.

If you have another suggestion on how to handle such situation, feel free to add it. Mine was just a potential suggestion on how to handle it.

All in all, It's no big deal to support -1, but could prevent some errors/exceptions, since I assume that the default value is an acceptable value.

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Updated as suggested.

parser.error("--compression-level must be an integer from 0 and 9")
else:
if options.compression_level:
parser.error("--compression-level option is only valid for jsongz file formats")

# -

return options
Expand Down Expand Up @@ -226,6 +247,43 @@ def json_writer(filename, fields, task_queue, error_queue, format):
pass


def jsongz_writer(filename, fields, task_queue, error_queue, format, compression_level):
try:
with open(filename, "wb") as out:
# wbits 31 = MAX_WBITS + gzip header and trailer
compressor = zlib.compressobj(compression_level, zlib.DEFLATED, 31)
def compress_and_write(str):
out.write(compressor.compress(str.encode("utf-8")))

first = True
compress_and_write("[")
item = task_queue.get()
while not isinstance(item, StopIteration):
row = item[0]
if fields is not None:
for item in list(row.keys()):
if item not in fields:
del row[item]
if first:
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This implies that the objects in the JSON array are each on a separate line.

I'm no compression expert, but since it'll be binary and unreadable from a high level perspective, why not skip the new line? Object would be written as follows
[{...},{...},{...}...{...}]
which would save n + 1 + 1 new lines (n-1 between each object, plus 2 for the first and the last, + 1 for the last row which EOF and is good. On huge table this could imply saving a considerable amount of bits. @gabor-boros do you have any knowledge about the topic?

Or maybe I'm wrong and the \n are used for compression. Let me know, I'm curious now.

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The code here is replicating what the json export does. \n are not used for compression.

One can still unpack the jsongz file get the json file from inside (it's a standard gzip file), in which case the formatting might help. I considered the gains from removing the \n-s marginal, but you might be right. If you have really small documents, the extra end lines might make a difference.

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@iantocristian iantocristian Mar 24, 2021 •
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Should say that import script includes a custom json paarser (which I found odd, not sure what the reason for using a custom parser was, performance perhaps?) which might be affected by the lack of new lines (I expect it to be happy though).

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if you have really small documents, the extra end lines might make a difference

Did you mean big documents? Hehe

Regarding the custom json parser, I have no clue why there's a custom one. Probably, when the library has been written, there were parsers that did not fit/match the requirements. Nowadays there are tons of high performance parsers. In order to not break anything, I would keep the custom one for now.

compress_and_write("\n")
first = False
else:
compress_and_write(",\n")

compress_and_write(json.dumps(row))
item = task_queue.get()

compress_and_write("\n]\n")
out.write(compressor.flush())
except BaseException:
ex_type, ex_class, tb = sys.exc_info()
error_queue.put((ex_type, ex_class, traceback.extract_tb(tb)))

# Read until the exit task so the readers do not hang on pushing onto the queue
while not isinstance(task_queue.get(), StopIteration):
pass


def csv_writer(filename, fields, delimiter, task_queue, error_queue):
try:
with open(filename, "w") as out:
Expand Down Expand Up @@ -331,6 +389,19 @@ def export_table(
options.format,
),
)
elif options.format == "jsongz":
filename = directory + "/%s/%s.jsongz" % (db, table)
writer = multiprocessing.Process(
target=jsongz_writer,
args=(
filename,
options.fields,
task_queue,
error_queue,
options.format,
options.compression_level,
),
)
elif options.format == "csv":
filename = directory + "/%s/%s.csv" % (db, table)
writer = multiprocessing.Process(
Expand Down
72 changes: 57 additions & 15 deletions rethinkdb/_import.py
100755 → 100644
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Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,11 @@
import optparse
import os
import signal
import struct
import sys
import time
import traceback
import zlib
from multiprocessing.queues import Queue, SimpleQueue

import six
Expand All @@ -56,6 +58,9 @@
JSON_MAX_BUFFER_SIZE = 128 * 1024 * 1024
MAX_NESTING_DEPTH = 100

# jsongz parameters
JSON_GZ_READ_CHUNK_SIZE = 16 * 1024

Error = collections.namedtuple("Error", ["message", "traceback", "file"])


Expand Down Expand Up @@ -133,7 +138,10 @@ def __init__(
self._source = source
else:
try:
self._source = codecs.open(source, mode="r", encoding="utf-8")
if self.format == "jsongz":
self._source = open(source, mode="rb")
else:
self._source = codecs.open(source, mode="r", encoding="utf-8")
except IOError as exc:
default_logger.exception(exc)
raise ValueError(
Expand All @@ -145,9 +153,16 @@ def __init__(
and self._source.name
and os.path.isfile(self._source.name)
):
self._bytes_size.value = os.path.getsize(source)
self._bytes_size.value = os.path.getsize(self._source.name)
if self._bytes_size.value == 0:
raise ValueError("Source is zero-length: %s" % source)
raise ValueError("Source is zero-length: %s" % self._source.name)

# get uncompressed file length from gzip trailer (last 4 bytes)
if self.format == "jsongz":
# TODO: check valid gzip
self._source.seek(-4, 2)
self._bytes_size.value = struct.unpack("I", self._source.read(4))[0]
self._source.seek(0)

# table info
self.db = db
Expand Down Expand Up @@ -500,6 +515,9 @@ class JsonSourceFile(SourceFile):
_buffer_pos = None
_buffer_end = None

def read_chunk(self, max_length):
return self._source.read(max_length)

def fill_buffer(self):
if self._buffer_str is None:
self._buffer_str = ""
Expand All @@ -520,7 +538,7 @@ def fill_buffer(self):
if read_target < 1:
raise AssertionError("Can not set the read target and full the buffer")

new_chunk = self._source.read(read_target)
new_chunk = self.read_chunk(read_target)

if len(new_chunk) == 0:
raise StopIteration() # file ended
Expand Down Expand Up @@ -634,6 +652,28 @@ def teardown(self):
)


class JsonGzSourceFile(JsonSourceFile):
format = "jsongz"

def __init__(self, *args, **kwargs):

# initialize zlib decompressor
# wbits 31 = window size MAX_WBITS & expects gzip header and trailer
self._decompressor = zlib.decompressobj(31)

super(JsonGzSourceFile, self).__init__(*args, **kwargs)

def read_chunk(self, max_length):
chunk = b''
while len(chunk) < max_length:
compressed_buf = self._decompressor.unconsumed_tail + self._source.read(JSON_GZ_READ_CHUNK_SIZE)
if len(compressed_buf) == 0:
break
decompressed_buf = self._decompressor.decompress(compressed_buf, max_length - len(chunk))
chunk += decompressed_buf
return chunk.decode("utf-8")


class CsvSourceFile(SourceFile):
format = "csv"

Expand Down Expand Up @@ -855,11 +895,11 @@ def parse_options(argv, prog=None):
file_import_group.add_option(
"--format",
dest="format",
metavar="json|csv",
metavar="json|jsongz|csv",
default=None,
help="format of the file (default: json, accepts newline delimited json)",
type="choice",
choices=["json", "csv"],
choices=["json", "jsongz", "csv"],
)
file_import_group.add_option(
"--pkey",
Expand Down Expand Up @@ -1036,7 +1076,7 @@ def parse_options(argv, prog=None):
if options.custom_header:
options.custom_header = options.custom_header.split(",")

elif options.format == "json":
elif (options.format == "json" or options.format == "jsongz") :
# disallow invalid options
if options.delimiter is not None:
parser.error("--delimiter option is not valid for json files")
Expand All @@ -1045,13 +1085,6 @@ def parse_options(argv, prog=None):
if options.custom_header is not None:
parser.error("--custom-header option is not valid for json files")

# default options
options.format = "json"

if options.max_document_size > 0:
global JSON_MAX_BUFFER_SIZE
JSON_MAX_BUFFER_SIZE = options.max_document_size

options.file = os.path.abspath(options.file)

else:
Expand All @@ -1062,6 +1095,11 @@ def parse_options(argv, prog=None):

# --

# max_document_size - json
if options.max_document_size > 0:
global JSON_MAX_BUFFER_SIZE
JSON_MAX_BUFFER_SIZE = options.max_document_size

# max_nesting_depth
if options.max_nesting_depth > 0:
global MAX_NESTING_DEPTH
Expand Down Expand Up @@ -1552,6 +1590,8 @@ def parse_info_file(path):
table_type_options = None
if ext == ".json":
table_type = JsonSourceFile
elif ext == ".jsongz":
table_type = JsonGzSourceFile
elif ext == ".csv":
table_type = CsvSourceFile
table_type_options = {
Expand Down Expand Up @@ -1622,7 +1662,7 @@ def parse_info_file(path):
table, ext = os.path.splitext(filename)
table = os.path.basename(table)

if ext not in [".json", ".csv", ".info"]:
if ext not in [".json", ".jsongz", ".csv", ".info"]:
files_ignored.append(os.path.join(root, filename))
elif ext == ".info":
pass # Info files are included based on the data files
Expand Down Expand Up @@ -1657,6 +1697,8 @@ def parse_info_file(path):
table_type = None
if ext == ".json":
table_type = JsonSourceFile
elif ext == ".jsongz":
table_type = JsonGzSourceFile
elif ext == ".csv":
table_type = CsvSourceFile
else:
Expand Down