/
pandas.py
1435 lines (1357 loc) · 69.1 KB
/
pandas.py
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from typing import Dict, List, Tuple, Optional, Any, Union
from io import BytesIO, StringIO
import multiprocessing as mp
import logging
from math import floor
import copy
import csv
from datetime import datetime, date
from decimal import Decimal
from ast import literal_eval
from botocore.exceptions import ClientError, HTTPClientError # type: ignore
import pandas as pd # type: ignore
import pyarrow as pa # type: ignore
from pyarrow import parquet as pq # type: ignore
import tenacity # type: ignore
from s3fs import S3FileSystem # type: ignore
from awswrangler import data_types
from awswrangler.exceptions import (UnsupportedWriteMode, UnsupportedFileFormat, AthenaQueryError, EmptyS3Object,
LineTerminatorNotFound, EmptyDataframe, InvalidSerDe, InvalidCompression,
InvalidParameters)
from awswrangler.utils import calculate_bounders
from awswrangler import s3
from awswrangler.athena import Athena
logger = logging.getLogger(__name__)
MIN_NUMBER_OF_ROWS_TO_DISTRIBUTE = 1000
def _get_bounders(dataframe, num_partitions):
num_rows = len(dataframe.index)
return calculate_bounders(num_items=num_rows, num_groups=num_partitions)
class Pandas:
VALID_CSV_SERDES = ["OpenCSVSerDe", "LazySimpleSerDe"]
VALID_CSV_COMPRESSIONS = [None]
VALID_PARQUET_COMPRESSIONS = [None, "snappy", "gzip"]
def __init__(self, session):
self._session = session
@staticmethod
def _parse_path(path):
path2 = path.replace("s3://", "")
parts = path2.partition("/")
return parts[0], parts[2]
def read_csv(
self,
path,
max_result_size=None,
header="infer",
names=None,
usecols=None,
dtype=None,
sep=",",
thousands=None,
decimal=".",
lineterminator="\n",
quotechar='"',
quoting=csv.QUOTE_MINIMAL,
escapechar=None,
parse_dates: Union[bool, Dict, List] = False,
infer_datetime_format=False,
encoding="utf-8",
converters=None,
):
"""
Read CSV file from AWS S3 using optimized strategies.
Try to mimic as most as possible pandas.read_csv()
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html
P.S. max_result_size != None tries to mimic the chunksize behaviour in pandas.read_sql()
:param path: AWS S3 path (E.g. S3://BUCKET_NAME/KEY_NAME)
:param max_result_size: Max number of bytes on each request to S3
:param header: Same as pandas.read_csv()
:param names: Same as pandas.read_csv()
:param usecols: Same as pandas.read_csv()
:param dtype: Same as pandas.read_csv()
:param sep: Same as pandas.read_csv()
:param thousands: Same as pandas.read_csv()
:param decimal: Same as pandas.read_csv()
:param lineterminator: Same as pandas.read_csv()
:param quotechar: Same as pandas.read_csv()
:param quoting: Same as pandas.read_csv()
:param escapechar: Same as pandas.read_csv()
:param parse_dates: Same as pandas.read_csv()
:param infer_datetime_format: Same as pandas.read_csv()
:param encoding: Same as pandas.read_csv()
:param converters: Same as pandas.read_csv()
:return: Pandas Dataframe or Iterator of Pandas Dataframes if max_result_size != None
"""
bucket_name, key_path = self._parse_path(path)
client_s3 = self._session.boto3_session.client(service_name="s3",
use_ssl=True,
config=self._session.botocore_config)
if max_result_size:
ret = Pandas._read_csv_iterator(client_s3=client_s3,
bucket_name=bucket_name,
key_path=key_path,
max_result_size=max_result_size,
header=header,
names=names,
usecols=usecols,
dtype=dtype,
sep=sep,
thousands=thousands,
decimal=decimal,
lineterminator=lineterminator,
quotechar=quotechar,
quoting=quoting,
escapechar=escapechar,
parse_dates=parse_dates,
infer_datetime_format=infer_datetime_format,
encoding=encoding,
converters=converters)
else:
ret = Pandas._read_csv_once(client_s3=client_s3,
bucket_name=bucket_name,
key_path=key_path,
header=header,
names=names,
usecols=usecols,
dtype=dtype,
sep=sep,
thousands=thousands,
decimal=decimal,
lineterminator=lineterminator,
quotechar=quotechar,
quoting=quoting,
escapechar=escapechar,
parse_dates=parse_dates,
infer_datetime_format=infer_datetime_format,
encoding=encoding,
converters=converters)
return ret
@staticmethod
def _read_csv_iterator(
client_s3,
bucket_name,
key_path,
max_result_size=200_000_000, # 200 MB
header="infer",
names=None,
usecols=None,
dtype=None,
sep=",",
thousands=None,
decimal=".",
lineterminator="\n",
quotechar='"',
quoting=csv.QUOTE_MINIMAL,
escapechar=None,
parse_dates: Union[bool, Dict, List] = False,
infer_datetime_format=False,
encoding="utf-8",
converters=None,
):
"""
Read CSV file from AWS S3 using optimized strategies.
Try to mimic as most as possible pandas.read_csv()
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html
:param client_s3: Boto3 S3 client object
:param bucket_name: S3 bucket name
:param key_path: S3 key path (W/o bucket)
:param max_result_size: Max number of bytes on each request to S3
:param header: Same as pandas.read_csv()
:param names: Same as pandas.read_csv()
:param usecols: Same as pandas.read_csv()
:param dtype: Same as pandas.read_csv()
:param sep: Same as pandas.read_csv()
:param thousands: Same as pandas.read_csv()
:param decimal: Same as pandas.read_csv()
:param lineterminator: Same as pandas.read_csv()
:param quotechar: Same as pandas.read_csv()
:param quoting: Same as pandas.read_csv()
:param escapechar: Same as pandas.read_csv()
:param parse_dates: Same as pandas.read_csv()
:param infer_datetime_format: Same as pandas.read_csv()
:param encoding: Same as pandas.read_csv()
:param converters: Same as pandas.read_csv()
:return: Pandas Dataframe
"""
metadata = s3.S3.head_object_with_retry(client=client_s3, bucket=bucket_name, key=key_path)
logger.debug(f"metadata: {metadata}")
total_size = metadata["ContentLength"]
logger.debug(f"total_size: {total_size}")
if total_size <= 0:
raise EmptyS3Object(metadata)
elif total_size <= max_result_size:
yield Pandas._read_csv_once(client_s3=client_s3,
bucket_name=bucket_name,
key_path=key_path,
header=header,
names=names,
usecols=usecols,
dtype=dtype,
sep=sep,
thousands=thousands,
decimal=decimal,
lineterminator=lineterminator,
quotechar=quotechar,
quoting=quoting,
escapechar=escapechar,
parse_dates=parse_dates,
infer_datetime_format=infer_datetime_format,
encoding=encoding,
converters=converters)
else:
bounders = calculate_bounders(num_items=total_size, max_size=max_result_size)
logger.debug(f"bounders: {bounders}")
bounders_len = len(bounders)
count = 0
forgotten_bytes = 0
for ini, end in bounders:
count += 1
ini -= forgotten_bytes
end -= 1 # Range is inclusive, contrary from Python's List
bytes_range = "bytes={}-{}".format(ini, end)
logger.debug(f"bytes_range: {bytes_range}")
body = client_s3.get_object(Bucket=bucket_name, Key=key_path, Range=bytes_range)["Body"].read()
chunk_size = len(body)
logger.debug(f"chunk_size (bytes): {chunk_size}")
if count == 1: # first chunk
last_char = Pandas._find_terminator(body=body,
sep=sep,
quoting=quoting,
quotechar=quotechar,
lineterminator=lineterminator)
forgotten_bytes = len(body[last_char:])
elif count == bounders_len: # Last chunk
last_char = chunk_size
else:
last_char = Pandas._find_terminator(body=body,
sep=sep,
quoting=quoting,
quotechar=quotechar,
lineterminator=lineterminator)
forgotten_bytes = len(body[last_char:])
df = pd.read_csv(StringIO(body[:last_char].decode("utf-8")),
header=header,
names=names,
usecols=usecols,
sep=sep,
thousands=thousands,
decimal=decimal,
quotechar=quotechar,
quoting=quoting,
escapechar=escapechar,
parse_dates=parse_dates,
infer_datetime_format=infer_datetime_format,
lineterminator=lineterminator,
dtype=dtype,
encoding=encoding,
converters=converters)
yield df
if count == 1: # first chunk
names = df.columns
header = None
@staticmethod
def _extract_terminator_profile(body, sep, quotechar, lineterminator, last_index):
"""
Backward parser for quoted CSV lines
:param body: String
:param sep: Same as pandas.read_csv()
:param quotechar: Same as pandas.read_csv()
:param lineterminator: Same as pandas.read_csv()
:return: Dict with the profile
"""
sep_int = int.from_bytes(bytes=sep.encode(encoding="utf-8"), byteorder="big") # b"," -> 44
quote_int = int.from_bytes(bytes=quotechar.encode(encoding="utf-8"), byteorder="big") # b'"' -> 34
terminator_int = int.from_bytes(bytes=lineterminator.encode(encoding="utf-8"), byteorder="big") # b"\n" -> 10
logger.debug(f"sep_int: {sep_int}")
logger.debug(f"quote_int: {quote_int}")
logger.debug(f"terminator_int: {terminator_int}")
last_terminator_suspect_index = None
first_non_special_byte_index = None
sep_counter = 0
quote_counter = 0
for i in range((len(body[:last_index]) - 1), -1, -1):
b = body[i]
if last_terminator_suspect_index:
if b == quote_int:
quote_counter += 1
elif b == sep_int:
sep_counter += 1
elif b == terminator_int:
pass
else:
first_non_special_byte_index = i
break
if b == terminator_int:
if not last_terminator_suspect_index:
last_terminator_suspect_index = i
elif last_terminator_suspect_index - 1 == i:
first_non_special_byte_index = i
break
logger.debug(f"last_terminator_suspect_index: {last_terminator_suspect_index}")
logger.debug(f"first_non_special_byte_index: {first_non_special_byte_index}")
logger.debug(f"sep_counter: {sep_counter}")
logger.debug(f"quote_counter: {quote_counter}")
return {
"last_terminator_suspect_index": last_terminator_suspect_index,
"first_non_special_byte_index": first_non_special_byte_index,
"sep_counter": sep_counter,
"quote_counter": quote_counter
}
@staticmethod
def _find_terminator(body, sep, quoting, quotechar, lineterminator):
"""
Find for any suspicious of line terminator (From end to start)
:param body: String
:param sep: Same as pandas.read_csv()
:param quoting: Same as pandas.read_csv()
:param quotechar: Same as pandas.read_csv()
:param lineterminator: Same as pandas.read_csv()
:return: The index of the suspect line terminator
"""
try:
last_index = None
if quoting == csv.QUOTE_ALL:
while True:
profile = Pandas._extract_terminator_profile(body=body,
sep=sep,
quotechar=quotechar,
lineterminator=lineterminator,
last_index=last_index)
if profile["last_terminator_suspect_index"] and profile["first_non_special_byte_index"]:
if profile["quote_counter"] % 2 == 0 or profile["quote_counter"] == 0:
last_index = profile["last_terminator_suspect_index"]
else:
index = profile["last_terminator_suspect_index"]
break
else:
raise LineTerminatorNotFound()
else:
index = body.rindex(lineterminator.encode(encoding="utf-8"))
except ValueError:
raise LineTerminatorNotFound()
return index
@staticmethod
def _read_csv_once(
client_s3,
bucket_name,
key_path,
header="infer",
names=None,
usecols=None,
dtype=None,
sep=",",
thousands=None,
decimal=".",
lineterminator="\n",
quotechar='"',
quoting=0,
escapechar=None,
parse_dates: Union[bool, Dict, List] = False,
infer_datetime_format=False,
encoding=None,
converters=None,
):
"""
Read CSV file from AWS S3 using optimized strategies.
Try to mimic as most as possible pandas.read_csv()
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html
:param client_s3: Boto3 S3 client object
:param bucket_name: S3 bucket name
:param key_path: S3 key path (W/o bucket)
:param header: Same as pandas.read_csv()
:param names: Same as pandas.read_csv()
:param usecols: Same as pandas.read_csv()
:param dtype: Same as pandas.read_csv()
:param sep: Same as pandas.read_csv()
:param thousands: Same as pandas.read_csv()
:param decimal: Same as pandas.read_csv()
:param lineterminator: Same as pandas.read_csv()
:param quotechar: Same as pandas.read_csv()
:param quoting: Same as pandas.read_csv()
:param escapechar: Same as pandas.read_csv()
:param parse_dates: Same as pandas.read_csv()
:param infer_datetime_format: Same as pandas.read_csv()
:param encoding: Same as pandas.read_csv()
:param converters: Same as pandas.read_csv()
:return: Pandas Dataframe
"""
buff = BytesIO()
client_s3.download_fileobj(Bucket=bucket_name, Key=key_path, Fileobj=buff)
buff.seek(0),
dataframe = pd.read_csv(
buff,
header=header,
names=names,
usecols=usecols,
sep=sep,
thousands=thousands,
decimal=decimal,
quotechar=quotechar,
quoting=quoting,
escapechar=escapechar,
parse_dates=parse_dates,
infer_datetime_format=infer_datetime_format,
lineterminator=lineterminator,
dtype=dtype,
encoding=encoding,
converters=converters,
)
buff.close()
return dataframe
@staticmethod
def _list_parser(value: str) -> List[Union[int, float, str, None]]:
# try resolve with a simple literal_eval
try:
return literal_eval(value)
except ValueError:
pass # keep trying
# sanity check
if len(value) <= 1:
return []
items: List[Union[None, str]] = [None if x == "null" else x for x in value[1:-1].split(", ")]
array_type: Optional[type] = None
# check if all values are integers
for item in items:
if item is not None:
try:
int(item) # type: ignore
except ValueError:
break
else:
array_type = int
# check if all values are floats
if array_type is None:
for item in items:
if item is not None:
try:
float(item) # type: ignore
except ValueError:
break
else:
array_type = float
# check if all values are strings
array_type = str if array_type is None else array_type
return [array_type(x) if x is not None else None for x in items]
def _get_query_dtype(self, query_execution_id: str) -> Tuple[Dict[str, str], List[str], List[str], Dict[str, Any]]:
cols_metadata: Dict[str, str] = self._session.athena.get_query_columns_metadata(
query_execution_id=query_execution_id)
logger.debug(f"cols_metadata: {cols_metadata}")
dtype: Dict[str, str] = {}
parse_timestamps: List[str] = []
parse_dates: List[str] = []
converters: Dict[str, Any] = {}
col_name: str
col_type: str
for col_name, col_type in cols_metadata.items():
pandas_type: str = data_types.athena2pandas(dtype=col_type)
if pandas_type in ["datetime64", "date"]:
parse_timestamps.append(col_name)
if pandas_type == "date":
parse_dates.append(col_name)
elif pandas_type == "list":
converters[col_name] = Pandas._list_parser
elif pandas_type == "bool":
logger.debug(f"Ignoring bool column: {col_name}")
elif pandas_type == "decimal":
converters[col_name] = lambda x: Decimal(str(x)) if str(x) != "" else None
else:
dtype[col_name] = pandas_type
logger.debug(f"dtype: {dtype}")
logger.debug(f"parse_timestamps: {parse_timestamps}")
logger.debug(f"parse_dates: {parse_dates}")
logger.debug(f"converters: {converters}")
return dtype, parse_timestamps, parse_dates, converters
def read_sql_athena(self,
sql: str,
database: Optional[str] = None,
s3_output: Optional[str] = None,
workgroup: Optional[str] = None,
encryption: Optional[str] = None,
kms_key: Optional[str] = None,
ctas_approach: bool = None,
procs_cpu_bound: Optional[int] = None,
max_result_size: Optional[int] = None):
"""
Executes any SQL query on AWS Athena and return a Dataframe of the result.
There are two approaches to be defined through ctas_approach parameter:
1 - ctas_approach True (For Huge results):
Wrap the query with a CTAS and then reads the table data as parquet directly from s3.
PROS: Faster and has a better handle of nested types
CONS: Can't use max_result_size and must have create and drop table permissions
2 - ctas_approach False (Default):
Does a regular query on Athena and parse the regular CSV result on s3
PROS: Accepts max_result_size.
CONS: Slower (But stills faster than other libraries that uses the Athena API) and does not handle nested types so well
P.S. If ctas_approach is False and max_result_size is passed, then a iterator of Dataframes is returned.
P.S.S. All default values will be inherited from the Session()
:param sql: SQL Query
:param database: Glue/Athena Database
:param s3_output: AWS S3 path
:param workgroup: The name of the workgroup in which the query is being started. (By default uses de Session() workgroup)
:param encryption: None|'SSE_S3'|'SSE_KMS'|'CSE_KMS'
:param kms_key: For SSE-KMS and CSE-KMS , this is the KMS key ARN or ID.
:param ctas_approach: Wraps the query with a CTAS (Session's default is False)
:param procs_cpu_bound: Number of cores used for CPU bound tasks
:param max_result_size: Max number of bytes on each request to S3 (VALID ONLY FOR ctas_approach=False)
:return: Pandas Dataframe or Iterator of Pandas Dataframes if max_result_size was passed
"""
ctas_approach = ctas_approach if ctas_approach is not None else self._session.athena_ctas_approach if self._session.athena_ctas_approach is not None else False
if ctas_approach is True and max_result_size is not None:
raise InvalidParameters("ctas_approach can't use max_result_size!")
if s3_output is None:
if self._session.athena_s3_output is not None:
s3_output = self._session.athena_s3_output
else:
s3_output = self._session.athena.create_athena_bucket()
if ctas_approach is False:
return self._read_sql_athena_regular(sql=sql,
database=database,
s3_output=s3_output,
workgroup=workgroup,
encryption=encryption,
kms_key=kms_key,
max_result_size=max_result_size)
else:
return self._read_sql_athena_ctas(sql=sql,
database=database,
s3_output=s3_output,
workgroup=workgroup,
encryption=encryption,
kms_key=kms_key,
procs_cpu_bound=procs_cpu_bound)
def _read_sql_athena_ctas(self,
sql: str,
s3_output: str,
database: Optional[str] = None,
workgroup: Optional[str] = None,
encryption: Optional[str] = None,
kms_key: Optional[str] = None,
procs_cpu_bound: Optional[int] = None) -> pd.DataFrame:
guid: str = pa.compat.guid()
name: str = f"temp_table_{guid}"
s3_output = s3_output[:-1] if s3_output[-1] == "/" else s3_output
path: str = f"{s3_output}/{name}"
query: str = f"CREATE TABLE {name}\n" \
f"WITH(\n" \
f" format = 'Parquet',\n" \
f" parquet_compression = 'SNAPPY',\n" \
f" external_location = '{path}'\n" \
f") AS\n" \
f"{sql}"
logger.debug(f"query: {query}")
query_id: str = self._session.athena.run_query(query=query,
database=database,
s3_output=s3_output,
workgroup=workgroup,
encryption=encryption,
kms_key=kms_key)
self._session.athena.wait_query(query_execution_id=query_id)
self._session.glue.delete_table_if_exists(database=database, table=name)
manifest_path: str = f"{s3_output}/tables/{query_id}-manifest.csv"
paths: List[str] = self._session.athena.extract_manifest_paths(path=manifest_path)
logger.debug(f"paths: {paths}")
return self.read_parquet(path=paths, procs_cpu_bound=procs_cpu_bound)
def _read_sql_athena_regular(self,
sql: str,
s3_output: str,
database: Optional[str] = None,
workgroup: Optional[str] = None,
encryption: Optional[str] = None,
kms_key: Optional[str] = None,
max_result_size: Optional[int] = None):
query_execution_id: str = self._session.athena.run_query(query=sql,
database=database,
s3_output=s3_output,
workgroup=workgroup,
encryption=encryption,
kms_key=kms_key)
query_response: Dict = self._session.athena.wait_query(query_execution_id=query_execution_id)
if query_response["QueryExecution"]["Status"]["State"] in ["FAILED", "CANCELLED"]:
reason: str = query_response["QueryExecution"]["Status"]["StateChangeReason"]
message_error: str = f"Query error: {reason}"
raise AthenaQueryError(message_error)
else:
dtype, parse_timestamps, parse_dates, converters = self._get_query_dtype(
query_execution_id=query_execution_id)
path = f"{s3_output}{query_execution_id}.csv"
ret = self.read_csv(path=path,
dtype=dtype,
parse_dates=parse_timestamps,
converters=converters,
quoting=csv.QUOTE_ALL,
max_result_size=max_result_size)
if max_result_size is None:
if len(ret.index) > 0:
for col in parse_dates:
if str(ret[col].dtype) == "object":
ret[col] = ret[col].apply(lambda x: date(*[int(y) for y in x.split("-")]))
else:
ret[col] = ret[col].dt.date.replace(to_replace={pd.NaT: None})
return ret
else:
return Pandas._apply_dates_to_generator(generator=ret, parse_dates=parse_dates)
@staticmethod
def _apply_dates_to_generator(generator, parse_dates):
for df in generator:
if len(df.index) > 0:
for col in parse_dates:
df[col] = df[col].dt.date.replace(to_replace={pd.NaT: None})
yield df
def to_csv(
self,
dataframe,
path,
sep=",",
serde="OpenCSVSerDe",
database: Optional[str] = None,
table=None,
partition_cols=None,
preserve_index=True,
mode="append",
procs_cpu_bound=None,
procs_io_bound=None,
inplace=True,
):
"""
Write a Pandas Dataframe as CSV files on S3
Optionally writes metadata on AWS Glue.
:param dataframe: Pandas Dataframe
:param path: AWS S3 path (E.g. s3://bucket-name/folder_name/
:param sep: Same as pandas.to_csv()
:param serde: SerDe library name (e.g. OpenCSVSerDe, LazySimpleSerDe)
:param database: AWS Glue Database name
:param table: AWS Glue table name
:param partition_cols: List of columns names that will be partitions on S3
:param preserve_index: Should preserve index on S3?
:param mode: "append", "overwrite", "overwrite_partitions"
:param procs_cpu_bound: Number of cores used for CPU bound tasks
:param procs_io_bound: Number of cores used for I/O bound tasks
:param inplace: True is cheapest (CPU and Memory) but False leaves your DataFrame intact
:return: List of objects written on S3
"""
if serde not in Pandas.VALID_CSV_SERDES:
raise InvalidSerDe(f"{serde} in not in the valid SerDe list ({Pandas.VALID_CSV_SERDES})")
extra_args = {"sep": sep, "serde": serde}
return self.to_s3(dataframe=dataframe,
path=path,
file_format="csv",
database=database,
table=table,
partition_cols=partition_cols,
preserve_index=preserve_index,
mode=mode,
compression=None,
procs_cpu_bound=procs_cpu_bound,
procs_io_bound=procs_io_bound,
extra_args=extra_args,
inplace=inplace)
def to_parquet(self,
dataframe,
path,
database: Optional[str] = None,
table=None,
partition_cols=None,
preserve_index=True,
mode="append",
compression="snappy",
procs_cpu_bound=None,
procs_io_bound=None,
cast_columns=None,
inplace=True):
"""
Write a Pandas Dataframe as parquet files on S3
Optionally writes metadata on AWS Glue.
:param dataframe: Pandas Dataframe
:param path: AWS S3 path (E.g. s3://bucket-name/folder_name/)
:param database: AWS Glue Database name
:param table: AWS Glue table name
:param partition_cols: List of columns names that will be partitions on S3
:param preserve_index: Should preserve index on S3?
:param mode: "append", "overwrite", "overwrite_partitions"
:param compression: None, snappy, gzip, lzo
:param procs_cpu_bound: Number of cores used for CPU bound tasks
:param procs_io_bound: Number of cores used for I/O bound tasks
:param cast_columns: Dictionary of columns names and Athena/Glue types to be casted (E.g. {"col name": "bigint", "col2 name": "int"})
:param inplace: True is cheapest (CPU and Memory) but False leaves your DataFrame intact
:return: List of objects written on S3
"""
return self.to_s3(dataframe=dataframe,
path=path,
file_format="parquet",
database=database,
table=table,
partition_cols=partition_cols,
preserve_index=preserve_index,
mode=mode,
compression=compression,
procs_cpu_bound=procs_cpu_bound,
procs_io_bound=procs_io_bound,
cast_columns=cast_columns,
inplace=inplace)
def to_s3(self,
dataframe: pd.DataFrame,
path: str,
file_format: str,
database: Optional[str] = None,
table: Optional[str] = None,
partition_cols=None,
preserve_index=True,
mode: str = "append",
compression=None,
procs_cpu_bound=None,
procs_io_bound=None,
cast_columns=None,
extra_args=None,
inplace: bool = True) -> List[str]:
"""
Write a Pandas Dataframe on S3
Optionally writes metadata on AWS Glue.
:param dataframe: Pandas Dataframe
:param path: AWS S3 path (E.g. s3://bucket-name/folder_name/
:param file_format: "csv" or "parquet"
:param database: AWS Glue Database name
:param table: AWS Glue table name
:param partition_cols: List of columns names that will be partitions on S3
:param preserve_index: Should preserve index on S3?
:param mode: "append", "overwrite", "overwrite_partitions"
:param compression: None, gzip, snappy, etc
:param procs_cpu_bound: Number of cores used for CPU bound tasks
:param procs_io_bound: Number of cores used for I/O bound tasks
:param cast_columns: Dictionary of columns names and Athena/Glue types to be casted. (E.g. {"col name": "bigint", "col2 name": "int"}) (Only for "parquet" file_format)
:param extra_args: Extra arguments specific for each file formats (E.g. "sep" for CSV)
:param inplace: True is cheapest (CPU and Memory) but False leaves your DataFrame intact
:return: List of objects written on S3
"""
if partition_cols is None:
partition_cols = []
if cast_columns is None:
cast_columns = {}
dataframe = Pandas.normalize_columns_names_athena(dataframe, inplace=inplace)
cast_columns = {Athena.normalize_column_name(k): v for k, v in cast_columns.items()}
logger.debug(f"cast_columns: {cast_columns}")
partition_cols = [Athena.normalize_column_name(x) for x in partition_cols]
logger.debug(f"partition_cols: {partition_cols}")
dataframe = Pandas.drop_duplicated_columns(dataframe=dataframe, inplace=inplace)
if compression is not None:
compression = compression.lower()
file_format = file_format.lower()
if file_format == "csv":
if compression not in Pandas.VALID_CSV_COMPRESSIONS:
raise InvalidCompression(
f"{compression} isn't a valid CSV compression. Try: {Pandas.VALID_CSV_COMPRESSIONS}")
elif file_format == "parquet":
if compression not in Pandas.VALID_PARQUET_COMPRESSIONS:
raise InvalidCompression(
f"{compression} isn't a valid PARQUET compression. Try: {Pandas.VALID_PARQUET_COMPRESSIONS}")
else:
raise UnsupportedFileFormat(file_format)
if dataframe.empty:
raise EmptyDataframe()
if ((mode == "overwrite") or ((mode == "overwrite_partitions") and # noqa
(not partition_cols))):
self._session.s3.delete_objects(path=path)
elif mode not in ["overwrite_partitions", "append"]:
raise UnsupportedWriteMode(mode)
objects_paths = self.data_to_s3(dataframe=dataframe,
path=path,
partition_cols=partition_cols,
preserve_index=preserve_index,
file_format=file_format,
mode=mode,
compression=compression,
procs_cpu_bound=procs_cpu_bound,
procs_io_bound=procs_io_bound,
cast_columns=cast_columns,
extra_args=extra_args)
if database:
self._session.glue.metadata_to_glue(dataframe=dataframe,
path=path,
objects_paths=objects_paths,
database=database,
table=table,
partition_cols=partition_cols,
preserve_index=preserve_index,
file_format=file_format,
mode=mode,
compression=compression,
cast_columns=cast_columns,
extra_args=extra_args)
return objects_paths
def data_to_s3(self,
dataframe,
path,
file_format,
partition_cols=None,
preserve_index=True,
mode="append",
compression=None,
procs_cpu_bound=None,
procs_io_bound=None,
cast_columns=None,
extra_args=None):
if not procs_cpu_bound:
procs_cpu_bound = self._session.procs_cpu_bound
if not procs_io_bound:
procs_io_bound = self._session.procs_io_bound
logger.debug(f"procs_cpu_bound: {procs_cpu_bound}")
logger.debug(f"procs_io_bound: {procs_io_bound}")
if path[-1] == "/":
path = path[:-1]
objects_paths = []
if procs_cpu_bound > 1:
bounders = _get_bounders(dataframe=dataframe, num_partitions=procs_cpu_bound)
procs = []
receive_pipes = []
for bounder in bounders:
receive_pipe, send_pipe = mp.Pipe()
proc = mp.Process(
target=self._data_to_s3_dataset_writer_remote,
args=(send_pipe, dataframe.iloc[bounder[0]:bounder[1], :], path, partition_cols, preserve_index,
compression, self._session.primitives, file_format, cast_columns, extra_args),
)
proc.daemon = False
proc.start()
procs.append(proc)
receive_pipes.append(receive_pipe)
for i in range(len(procs)):
objects_paths += receive_pipes[i].recv()
procs[i].join()
receive_pipes[i].close()
else:
objects_paths += self._data_to_s3_dataset_writer(dataframe=dataframe,
path=path,
partition_cols=partition_cols,
preserve_index=preserve_index,
compression=compression,
session_primitives=self._session.primitives,
file_format=file_format,
cast_columns=cast_columns,
extra_args=extra_args)
if mode == "overwrite_partitions" and partition_cols:
if procs_io_bound > procs_cpu_bound:
num_procs = floor(float(procs_io_bound) / float(procs_cpu_bound))
else:
num_procs = 1
logger.debug(f"num_procs for delete_not_listed_objects: {num_procs}")
self._session.s3.delete_not_listed_objects(objects_paths=objects_paths, procs_io_bound=num_procs)
return objects_paths
@staticmethod
def _data_to_s3_dataset_writer(dataframe,
path,
partition_cols,
preserve_index,
compression,
session_primitives,
file_format,
cast_columns=None,
extra_args=None,
isolated_dataframe=False):
objects_paths = []
dataframe = Pandas._cast_pandas(dataframe=dataframe, cast_columns=cast_columns)
cast_columns_materialized = {c: t for c, t in cast_columns.items() if c not in partition_cols}
if not partition_cols:
object_path = Pandas._data_to_s3_object_writer(dataframe=dataframe,
path=path,
preserve_index=preserve_index,
compression=compression,
session_primitives=session_primitives,
file_format=file_format,
cast_columns=cast_columns_materialized,
extra_args=extra_args,
isolated_dataframe=isolated_dataframe)
objects_paths.append(object_path)
else:
dataframe = Pandas._cast_pandas(dataframe=dataframe, cast_columns=cast_columns)
for keys, subgroup in dataframe.groupby(partition_cols):
subgroup = subgroup.drop(partition_cols, axis="columns")
if not isinstance(keys, tuple):
keys = (keys, )
subdir = "/".join([f"{name}={val}" for name, val in zip(partition_cols, keys)])
prefix = "/".join([path, subdir])
object_path = Pandas._data_to_s3_object_writer(dataframe=subgroup,
path=prefix,
preserve_index=preserve_index,
compression=compression,
session_primitives=session_primitives,
file_format=file_format,
cast_columns=cast_columns_materialized,
extra_args=extra_args,
isolated_dataframe=True)
objects_paths.append(object_path)
return objects_paths
@staticmethod
def _cast_pandas(dataframe: pd.DataFrame, cast_columns: Dict[str, str]) -> pd.DataFrame:
for col, athena_type in cast_columns.items():
pandas_type: str = data_types.athena2pandas(dtype=athena_type)
if pandas_type == "datetime64":
dataframe[col] = pd.to_datetime(dataframe[col])
elif pandas_type == "date":
dataframe[col] = pd.to_datetime(dataframe[col]).dt.date.replace(to_replace={pd.NaT: None})
else:
dataframe[col] = dataframe[col].astype(pandas_type, skipna=True)
return dataframe
@staticmethod
def _data_to_s3_dataset_writer_remote(send_pipe,
dataframe,
path,
partition_cols,
preserve_index,
compression,
session_primitives,
file_format,
cast_columns=None,
extra_args=None):
send_pipe.send(
Pandas._data_to_s3_dataset_writer(dataframe=dataframe,
path=path,
partition_cols=partition_cols,
preserve_index=preserve_index,
compression=compression,
session_primitives=session_primitives,
file_format=file_format,
cast_columns=cast_columns,
extra_args=extra_args,
isolated_dataframe=True))
send_pipe.close()
@staticmethod
def _data_to_s3_object_writer(dataframe,
path,
preserve_index,
compression,
session_primitives,
file_format,
cast_columns=None,
extra_args=None,
isolated_dataframe=False):
fs = s3.get_fs(session_primitives=session_primitives)
fs = pa.filesystem._ensure_filesystem(fs)
s3.mkdir_if_not_exists(fs, path)
if compression is None:
compression_end = ""
elif compression == "snappy":
compression_end = ".snappy"
elif compression == "gzip":
compression_end = ".gz"
else:
raise InvalidCompression(compression)
guid = pa.compat.guid()
if file_format == "parquet":
outfile = f"{guid}.parquet{compression_end}"
elif file_format == "csv":
outfile = f"{guid}.csv{compression_end}"
else:
raise UnsupportedFileFormat(file_format)
object_path = "/".join([path, outfile])
if file_format == "parquet":
Pandas.write_parquet_dataframe(dataframe=dataframe,
path=object_path,
preserve_index=preserve_index,
compression=compression,