Update multiprocess to handle large numbers of output files

This commit is contained in:
Watchful1 2023-03-06 20:37:15 -08:00
parent 8dcc65abf7
commit 1f7a3137f4

View file

@ -24,9 +24,10 @@ import sys
import time
import argparse
import re
from datetime import datetime
from collections import defaultdict
import logging.handlers
import multiprocessing
from enum import Enum
# sets up logging to the console as well as a file
@ -34,9 +35,9 @@ log = logging.getLogger("bot")
log.setLevel(logging.INFO)
log_formatter = logging.Formatter('%(asctime)s - %(levelname)s: %(message)s')
log_stderr_handler = logging.StreamHandler()
log_stderr_handler.setFormatter(log_formatter)
log.addHandler(log_stderr_handler)
log_str_handler = logging.StreamHandler()
log_str_handler.setFormatter(log_formatter)
log.addHandler(log_str_handler)
if not os.path.exists("logs"):
os.makedirs("logs")
log_file_handler = logging.handlers.RotatingFileHandler(
@ -45,6 +46,19 @@ log_file_handler.setFormatter(log_formatter)
log.addHandler(log_file_handler)
class FileType(Enum):
COMMENT = 1
SUBMISSION = 2
@staticmethod
def to_str(file_type):
if file_type == FileType.COMMENT:
return "comments"
elif file_type == FileType.SUBMISSION:
return "submissions"
return "other"
# convenience object used to pass status information between processes
class FileConfig:
def __init__(self, input_path, output_path=None, complete=False, lines_processed=0, error_lines=0, lines_matched=0):
@ -57,6 +71,13 @@ class FileConfig:
self.error_message = None
self.error_lines = error_lines
self.lines_matched = lines_matched
file_name = os.path.split(input_path)[1]
if file_name.startswith("RS"):
self.file_type = FileType.SUBMISSION
elif file_name.startswith("RC"):
self.file_type = FileType.COMMENT
else:
raise ValueError(f"Unknown working file type: {file_name}")
def __str__(self):
return f"{self.input_path} : {self.output_path} : {self.file_size} : {self.complete} : {self.bytes_processed} : {self.lines_processed}"
@ -64,18 +85,29 @@ class FileConfig:
# another convenience object to read and write from both zst files and ndjson files
class FileHandle:
def __init__(self, path):
self.path = path
if self.path.endswith(".zst"):
self.is_compressed = True
elif self.path.endswith(".ndjson"):
self.is_compressed = False
else:
raise TypeError(f"File type not supported for writing {self.path}")
newline_encoded = "\n".encode('utf-8')
ext_len = len(".zst")
self.write_handle = None
self.other_handle = None
self.newline_encoded = "\n".encode('utf-8')
def __init__(self, path, is_split=False):
self.path = path
self.is_split = is_split
self.handles = {}
def get_paths(self, character_filter=None):
if self.is_split:
paths = []
for file in os.listdir(self.path):
if not file.endswith(".zst"):
continue
if character_filter is not None and character_filter != file[-FileHandle.ext_len - 1:-FileHandle.ext_len]:
continue
paths.append(os.path.join(self.path, file))
return paths
else:
return [self.path]
def get_count_files(self):
return len(self.get_paths())
# recursively decompress and decode a chunk of bytes. If there's a decode error then read another chunk and try with that, up to a limit of max_window_size bytes
@staticmethod
@ -93,9 +125,16 @@ class FileHandle:
# open a zst compressed ndjson file, or a regular uncompressed ndjson file and yield lines one at a time
# also passes back file progress
def yield_lines(self):
if self.is_compressed:
with open(self.path, 'rb') as file_handle:
def yield_lines(self, character_filter=None):
if self.is_split:
if character_filter is not None:
path = os.path.join(self.path, f"{character_filter}.zst")
else:
raise ValueError(f"{self.path} is split but no filter passed")
else:
path = self.path
if os.path.exists(path):
with open(path, 'rb') as file_handle:
buffer = ''
reader = zstandard.ZstdDecompressor(max_window_size=2**31).stream_reader(file_handle)
while True:
@ -110,34 +149,38 @@ class FileHandle:
buffer = lines[-1]
reader.close()
else:
with open(self.path, 'r') as file_handle:
line = file_handle.readline()
while line:
yield line.rstrip('\n'), file_handle.tell()
line = file_handle.readline()
# get either the main write handle or the character filter one, opening a new handle as needed
def get_write_handle(self, character_filter=None):
if character_filter is None:
character_filter = 1 # use 1 as the default name since ints hash quickly
handle = self.handles.get(character_filter)
if handle is None:
if character_filter == 1:
path = self.path
else:
if not os.path.exists(self.path):
os.makedirs(self.path)
path = os.path.join(self.path, f"{character_filter}.zst")
handle = zstandard.ZstdCompressor().stream_writer(open(path, 'wb'))
self.handles[character_filter] = handle
return handle
# write a line, opening the appropriate handle
def write_line(self, line):
if self.write_handle is None:
if self.is_compressed:
self.other_handle = open(self.path, 'wb')
self.write_handle = zstandard.ZstdCompressor().stream_writer(self.other_handle)
else:
self.write_handle = open(self.path, 'w', encoding="utf-8")
if self.is_compressed:
self.write_handle.write(line.encode('utf-8'))
self.write_handle.write(self.newline_encoded)
def write_line(self, line, value=None):
if self.is_split:
if value is None:
raise ValueError(f"{self.path} is split but no value passed")
character_filter = value[:1]
handle = self.get_write_handle(character_filter)
else:
self.write_handle.write(line)
self.write_handle.write("\n")
handle = self.get_write_handle()
handle.write(line.encode('utf-8'))
handle.write(FileHandle.newline_encoded)
def close(self):
if self.write_handle:
self.write_handle.close()
if self.other_handle:
self.other_handle.close()
for handle in self.handles.values():
handle.close()
# used for calculating running average of read speed
@ -157,16 +200,21 @@ class Queue:
# save file information and progress to a json file
# we don't want to save the whole FileConfig object, since some info resets if we restart
def save_file_list(input_files, working_folder, status_json, arg_string, script_type):
def save_file_list(input_files, working_folder, status_json, arg_string, script_type, completed_prefixes=None):
if not os.path.exists(working_folder):
os.makedirs(working_folder)
simple_file_list = []
for file in input_files:
simple_file_list.append([file.input_path, file.output_path, file.complete, file.lines_processed, file.error_lines, file.lines_matched])
if completed_prefixes is None:
completed_prefixes = []
else:
completed_prefixes = sorted([prefix for prefix in completed_prefixes])
with open(status_json, 'w') as status_json_file:
output_dict = {
"args": arg_string,
"type": script_type,
"completed_prefixes": completed_prefixes,
"files": simple_file_list,
}
status_json_file.write(json.dumps(output_dict, indent=4))
@ -182,18 +230,21 @@ def load_file_list(status_json):
input_files.append(
FileConfig(simple_file[0], simple_file[1], simple_file[2], simple_file[3], simple_file[4], simple_file[5])
)
return input_files, output_dict["args"], output_dict["type"]
completed_prefixes = set()
for prefix in output_dict["completed_prefixes"]:
completed_prefixes.add(prefix)
return input_files, output_dict["args"], output_dict["type"], completed_prefixes
else:
return None, None, None
return None, None, None, set()
# base of each separate process. Loads a file, iterates through lines and writes out
# the ones where the `field` of the object matches `value`. Also passes status
# information back to the parent via a queue
def process_file(file, queue, field, value, values):
def process_file(file, queue, field, value, values, split_intermediate):
queue.put(file)
input_handle = FileHandle(file.input_path)
output_handle = FileHandle(file.output_path)
output_handle = FileHandle(file.output_path, is_split=split_intermediate)
try:
for line, file_bytes_processed in input_handle.yield_lines():
try:
@ -207,7 +258,7 @@ def process_file(file, queue, field, value, values):
matched = True
if matched:
output_handle.write_line(line)
output_handle.write_line(line, observed)
file.lines_matched += 1
except (KeyError, json.JSONDecodeError) as err:
file.error_lines += 1
@ -227,15 +278,14 @@ def process_file(file, queue, field, value, values):
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Use multiple processes to decompress and iterate over pushshift dump files")
parser.add_argument("input", help="The input folder to recursively read files from")
parser.add_argument("--split", help="Split the output into separate files by the filter fields, only applies if there's multiple fields", action='store_const', const=True, default=True)
parser.add_argument("--output", help="Put the output files in this folder", default="")
parser.add_argument("--working", help="The folder to store temporary files in", default="pushshift_working")
parser.add_argument("--field", help="When deciding what lines to keep, use this field for comparisons", default="subreddit")
parser.add_argument("--value", help="When deciding what lines to keep, compare the field to this value. Supports a comma separated list. This is case sensitive", default="pushshift")
parser.add_argument("--value_list", help="A file of newline separated values to use. Overrides the value param if it is set", default=None)
parser.add_argument("--processes", help="Number of processes to use", default=10, type=int)
parser.add_argument("--file_filter", help="Regex filenames have to match to be processed", default="^rc_|rs_")
parser.add_argument("--compress_intermediate", help="Compress the intermediate files, use if the filter will result in a very large amount of data", action="store_true")
parser.add_argument("--file_filter", help="Regex filenames have to match to be processed", default="^RC_|RS_")
parser.add_argument("--split_intermediate", help="Split the intermediate files by the first letter of the matched field, use if the filter will result in a large number of separate files", action="store_true")
parser.add_argument(
"--error_rate", help=
"Percentage as an integer from 0 to 100 of the lines where the field can be missing. For the subreddit field especially, "
@ -282,7 +332,7 @@ if __name__ == '__main__':
multiprocessing.set_start_method('spawn')
queue = multiprocessing.Manager().Queue()
status_json = os.path.join(args.working, "status.json")
input_files, saved_arg_string, saved_type = load_file_list(status_json)
input_files, saved_arg_string, saved_type, completed_prefixes = load_file_list(status_json)
if saved_arg_string and saved_arg_string != arg_string:
log.warning(f"Args don't match args from json file. Delete working folder")
sys.exit(0)
@ -297,20 +347,20 @@ if __name__ == '__main__':
for subdir, dirs, files in os.walk(args.input):
files.sort()
for file_name in files:
if file_name.endswith(".zst") and re.search(args.file_filter, file_name, re.IGNORECASE) is not None:
if file_name.endswith(".zst") and re.search(args.file_filter, file_name) is not None:
input_path = os.path.join(subdir, file_name)
output_path = os.path.join(args.working, f"{file_name[:-4]}.{('zst' if args.compress_intermediate else 'ndjson')}")
if args.split_intermediate:
output_extension = ""
else:
output_extension = ".zst"
output_path = os.path.join(args.working, f"{file_name[:-4]}{output_extension}")
input_files.append(FileConfig(input_path, output_path=output_path))
save_file_list(input_files, args.working, status_json, arg_string, script_type)
else:
log.info(f"Existing input file was read, if this is not correct you should delete the {args.working} folder and run this script again")
files_processed = 0
total_bytes = 0
total_bytes_processed = 0
total_lines_processed = 0
total_lines_errored = 0
files_processed, total_bytes, total_bytes_processed, total_lines_processed, total_lines_matched, total_lines_errored = 0, 0, 0, 0, 0, 0
files_to_process = []
# calculate the total file size for progress reports, build a list of incomplete files to process
# do this largest to smallest by file size so that we aren't processing a few really big files with only a few threads at the end
@ -319,6 +369,7 @@ if __name__ == '__main__':
if file.complete:
files_processed += 1
total_lines_processed += file.lines_processed
total_lines_matched += file.lines_matched
total_bytes_processed += file.file_size
total_lines_errored += file.error_lines
else:
@ -335,7 +386,7 @@ if __name__ == '__main__':
log.info(f"Processing file: {file.input_path}")
# start the workers
with multiprocessing.Pool(processes=min(args.processes, len(files_to_process))) as pool:
workers = pool.starmap_async(process_file, [(file, queue, args.field, value, values) for file in files_to_process], chunksize=1, error_callback=log.info)
workers = pool.starmap_async(process_file, [(file, queue, args.field, value, values, args.split_intermediate) for file in files_to_process], chunksize=1, error_callback=log.info)
while not workers.ready() or not queue.empty():
# loop until the workers are all done, pulling in status messages as they are sent
file_update = queue.get()
@ -349,13 +400,7 @@ if __name__ == '__main__':
# I'm going to assume that the list of files is short enough that it's no
# big deal to just iterate each time since that saves a bunch of work
total_lines_processed = 0
total_lines_matched = 0
total_bytes_processed = 0
total_lines_errored = 0
files_processed = 0
files_errored = 0
i = 0
total_lines_processed, total_lines_matched, total_bytes_processed, total_lines_errored, files_processed, files_errored, i = 0, 0, 0, 0, 0, 0, 0
for file in input_files:
if file.input_path == file_update.input_path:
input_files[i] = file_update
@ -389,8 +434,10 @@ if __name__ == '__main__':
log.info(f"{total_lines_processed:,}, {total_lines_errored} errored : {(total_bytes_processed / (2**30)):.2f} gb, {(total_bytes_processed / total_bytes) * 100:.0f}% : {files_processed}/{len(input_files)}")
working_file_paths = []
type_handles = defaultdict(list)
prefixes = set()
count_incomplete = 0
count_intermediate_files = 0
# build a list of output files to combine
for file in sorted(input_files, key=lambda item: os.path.split(item.output_path)[1]):
if not file.complete:
@ -405,68 +452,94 @@ if __name__ == '__main__':
f"File {file.input_path} has {file.error_lines:,} errored lines out of {file.lines_processed:,}, "
f"{(file.error_lines / file.lines_processed) * (args.error_rate * 0.01):.2f}% which is above the limit of {args.error_rate}%")
count_incomplete += 1
elif file.output_path is not None:
if os.path.exists(file.output_path):
working_file_paths.append(file.output_path)
elif file.output_path is not None and os.path.exists(file.output_path):
input_handle = FileHandle(file.output_path, is_split=args.split_intermediate)
for path in input_handle.get_paths():
prefixes.add(path[-FileHandle.ext_len - 1:-FileHandle.ext_len])
count_intermediate_files += 1
type_handles[file.file_type].append(input_handle)
if count_incomplete > 0:
log.info(f"{count_incomplete} files were not completed, errored or don't exist, something went wrong. Aborting")
sys.exit()
log.info(f"Processing complete, combining {len(working_file_paths)} result files")
log.info(f"Processing complete, combining {count_intermediate_files} result files")
for completed_prefix in completed_prefixes:
if completed_prefix in prefixes:
prefixes.remove(completed_prefix)
output_lines = 0
all_handles = []
output_handles = {}
files_combined = 0
if args.split and values:
if values:
split = True
else:
split = False
for working_file_path in working_file_paths:
files_combined += 1
log.info(f"From {files_combined}/{len(working_file_paths)} files to {len(all_handles):,} output handles : {output_lines:,} lines : {os.path.split(working_file_path)[1]}")
working_file_name = os.path.split(working_file_path)[1]
if working_file_name.startswith("RS"):
file_type = "submissions"
elif working_file_name.startswith("RC"):
file_type = "comments"
else:
log.warning(f"Unknown working file type, skipping: {working_file_name}")
continue
input_handle = FileHandle(working_file_path)
if file_type not in output_handles:
output_handles[file_type] = {}
file_type_handles = output_handles[file_type]
if args.split_intermediate:
for prefix in sorted(prefixes):
log.info(f"From {files_combined}/{count_intermediate_files} files to {len(output_handles):,} output handles : {output_lines:,}/{total_lines_matched:,} lines")
for file_type, input_handles in type_handles.items():
for input_handle in input_handles:
has_lines = False
for line, file_bytes_processed in input_handle.yield_lines(character_filter=prefix):
if not has_lines:
has_lines = True
files_combined += 1
output_lines += 1
obj = json.loads(line)
observed_case = obj[args.field]
observed = observed_case.lower()
if observed not in output_handles:
if args.output:
if not os.path.exists(args.output):
os.makedirs(args.output)
output_file_path = os.path.join(args.output, f"{observed_case}_{FileType.to_str(file_type)}.zst")
else:
output_file_path = f"{observed_case}_{FileType.to_str(file_type)}.zst"
log.debug(f"Writing to file {output_file_path}")
output_handle = FileHandle(output_file_path)
output_handles[observed] = output_handle
else:
output_handle = output_handles[observed]
for line, file_bytes_processed in input_handle.yield_lines():
output_lines += 1
if split:
obj = json.loads(line)
observed_case = obj[args.field]
else:
observed_case = value
observed = observed_case.lower()
if observed not in file_type_handles:
if args.output:
if not os.path.exists(args.output):
os.makedirs(args.output)
output_file_path = os.path.join(args.output, f"{observed_case}_{file_type}.zst")
else:
output_file_path = f"{observed_case}_{file_type}.zst"
log.debug(f"Writing to file {output_file_path}")
output_handle = FileHandle(output_file_path)
file_type_handles[observed] = output_handle
all_handles.append(output_handle)
else:
output_handle = file_type_handles[observed]
output_handle.write_line(line)
if output_lines % 1000000 == 0:
log.info(f"From {files_combined}/{count_intermediate_files} files to {len(output_handles):,} output handles : {output_lines:,}/{total_lines_matched:,} lines : {input_handle.path} / {prefix}")
for handle in output_handles.values():
handle.close()
output_handles = {}
completed_prefixes.add(prefix)
save_file_list(input_files, args.working, status_json, arg_string, script_type, completed_prefixes)
output_handle.write_line(line)
if output_lines % 100000 == 0:
log.info(f"From {files_combined}/{len(working_file_paths)} files to {len(all_handles):,} output handles : {output_lines:,} lines : {os.path.split(working_file_path)[1]}")
else:
log.info(f"From {files_combined}/{count_intermediate_files} files to {len(output_handles):,} output handles : {output_lines:,}/{total_lines_matched:,} lines")
for file_type, input_handles in type_handles.items():
for input_handle in input_handles:
files_combined += 1
for line, file_bytes_processed in input_handle.yield_lines():
output_lines += 1
obj = json.loads(line)
observed_case = obj[args.field]
observed = observed_case.lower()
if observed not in output_handles:
if args.output:
if not os.path.exists(args.output):
os.makedirs(args.output)
output_file_path = os.path.join(args.output, f"{observed_case}_{FileType.to_str(file_type)}.zst")
else:
output_file_path = f"{observed_case}_{FileType.to_str(file_type)}.zst"
log.debug(f"Writing to file {output_file_path}")
output_handle = FileHandle(output_file_path)
output_handles[observed] = output_handle
else:
output_handle = output_handles[observed]
log.info(f"From {files_combined}/{len(working_file_paths)} files to {len(all_handles):,} output handles : {output_lines:,} lines")
for handle in all_handles:
handle.close()
output_handle.write_line(line)
if output_lines % 1000000 == 0:
log.info(f"From {files_combined}/{count_intermediate_files} files to {len(output_handles):,} output handles : {output_lines:,}/{total_lines_matched:,} lines : {input_handle.path}")
for handle in output_handles.values():
handle.close()
output_handles = {}
log.info(f"Finished combining files, {output_lines:,} lines written")
log.info(f"From {files_combined}/{count_intermediate_files} files to {len(output_handles):,} output handles : {output_lines:,}/{total_lines_matched:,} lines")