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#!/usr/bin/env python3
"""
Commands for backfilling content from bulk files into postgresql and s3 (minio).
Normally this is done by workers (in sandcrawler_worker.py) consuming from
Kafka feeds, but sometimes we have bulk processing output we want to backfill.
"""
import os
import sys
import argparse
import datetime
from sandcrawler import *
from sandcrawler.persist import *
def run_cdx(args):
worker = PersistCdxWorker(
db_url=args.db_url,
)
filter_mimetypes = ['application/pdf']
if args.no_mimetype_filter:
filter_mimetypes = None
pusher = CdxLinePusher(
worker,
args.cdx_file,
filter_http_statuses=[200, 226],
filter_mimetypes=filter_mimetypes,
#allow_octet_stream
batch_size=200,
)
pusher.run()
def run_grobid(args):
worker = PersistGrobidWorker(
db_url=args.db_url,
s3_url=args.s3_url,
s3_bucket=args.s3_bucket,
s3_access_key=args.s3_access_key,
s3_secret_key=args.s3_secret_key,
s3_only=args.s3_only,
db_only=args.db_only,
)
pusher = JsonLinePusher(
worker,
args.json_file,
batch_size=50,
)
pusher.run()
def run_grobid_disk(args):
"""
Writes XML to individual files on disk, and also prints non-XML metadata to
stdout as JSON, which can be redirected to a separate file.
"""
worker = PersistGrobidDiskWorker(
output_dir=args.output_dir,
)
pusher = JsonLinePusher(
worker,
args.json_file,
)
pusher.run()
def run_pdftrio(args):
worker = PersistPdfTrioWorker(
db_url=args.db_url,
)
pusher = JsonLinePusher(
worker,
args.json_file,
batch_size=100,
)
pusher.run()
def run_pdftext(args):
worker = PersistPdfTextWorker(
db_url=args.db_url,
s3_url=args.s3_url,
s3_bucket=args.s3_bucket,
s3_access_key=args.s3_access_key,
s3_secret_key=args.s3_secret_key,
s3_only=args.s3_only,
db_only=args.db_only,
)
pusher = JsonLinePusher(
worker,
args.json_file,
batch_size=50,
)
pusher.run()
def run_ingest_file_result(args):
worker = PersistIngestFileResultWorker(
db_url=args.db_url,
)
pusher = JsonLinePusher(
worker,
args.json_file,
batch_size=200,
)
pusher.run()
def run_ingest_request(args):
worker = PersistIngestRequestWorker(
db_url=args.db_url,
)
pusher = JsonLinePusher(
worker,
args.json_file,
batch_size=200,
)
pusher.run()
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--db-url',
help="postgresql database connection string",
default="postgres:///sandcrawler")
parser.add_argument('--s3-url',
help="S3 (minio) backend URL",
default="localhost:9000")
parser.add_argument('--s3-access-key',
help="S3 (minio) credential",
default=os.environ.get('MINIO_ACCESS_KEY'))
parser.add_argument('--s3-secret-key',
help="S3 (minio) credential",
default=os.environ.get('MINIO_SECRET_KEY'))
parser.add_argument('--s3-bucket',
help="S3 (minio) bucket to persist into",
default="sandcrawler-dev")
subparsers = parser.add_subparsers()
sub_cdx = subparsers.add_parser('cdx',
help="backfill a CDX file into postgresql cdx table")
sub_cdx.set_defaults(func=run_cdx)
sub_cdx.add_argument('cdx_file',
help="CDX file to import from (or '-' for stdin)",
type=argparse.FileType('r'))
sub_cdx.add_argument('--no-mimetype-filter',
action='store_true',
help="ignore mimetype filtering; insert all content types (eg, assuming pre-filtered)")
sub_grobid = subparsers.add_parser('grobid',
help="backfill a grobid JSON ('pg') dump into postgresql and s3 (minio)")
sub_grobid.set_defaults(func=run_grobid)
sub_grobid.add_argument('json_file',
help="grobid file to import from (or '-' for stdin)",
type=argparse.FileType('r'))
sub_grobid.add_argument('--s3-only',
action='store_true',
help="only upload TEI-XML to S3 (don't write to database)")
sub_grobid.add_argument('--db-only',
action='store_true',
help="only write status to sandcrawler-db (don't save TEI-XML to S3)")
sub_pdftext = subparsers.add_parser('pdftext',
help="backfill a pdftext JSON ('pg') dump into postgresql and s3 (minio)")
sub_pdftext.set_defaults(func=run_pdftext)
sub_pdftext.add_argument('json_file',
help="pdftext file to import from (or '-' for stdin)",
type=argparse.FileType('r'))
sub_pdftext.add_argument('--s3-only',
action='store_true',
help="only upload TEI-XML to S3 (don't write to database)")
sub_pdftext.add_argument('--db-only',
action='store_true',
help="only write status to sandcrawler-db (don't save TEI-XML to S3)")
sub_grobid_disk = subparsers.add_parser('grobid-disk',
help="dump GRBOID output to (local) files on disk")
sub_grobid_disk.set_defaults(func=run_grobid_disk)
sub_grobid_disk.add_argument('json_file',
help="grobid file to import from (or '-' for stdin)",
type=argparse.FileType('r'))
sub_grobid_disk.add_argument('output_dir',
help="base directory to output into",
type=str)
sub_pdftrio = subparsers.add_parser('pdftrio',
help="backfill a pdftrio JSON ('pg') dump into postgresql and s3 (minio)")
sub_pdftrio.set_defaults(func=run_pdftrio)
sub_pdftrio.add_argument('json_file',
help="pdftrio file to import from (or '-' for stdin)",
type=argparse.FileType('r'))
sub_ingest_file_result = subparsers.add_parser('ingest-file-result',
help="backfill a ingest_file_result JSON dump into postgresql")
sub_ingest_file_result.set_defaults(func=run_ingest_file_result)
sub_ingest_file_result.add_argument('json_file',
help="ingest_file_result file to import from (or '-' for stdin)",
type=argparse.FileType('r'))
sub_ingest_request = subparsers.add_parser('ingest-request',
help="backfill a ingest_request JSON dump into postgresql")
sub_ingest_request.set_defaults(func=run_ingest_request)
sub_ingest_request.add_argument('json_file',
help="ingest_request to import from (or '-' for stdin)",
type=argparse.FileType('r'))
args = parser.parse_args()
if not args.__dict__.get("func"):
print("Tell me what to do!", file=sys.stderr)
sys.exit(-1)
args.func(args)
if __name__ == '__main__':
main()
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