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#!/usr/bin/env python3
"""
Commands for backfilling content from bulk files into postgresql and s3 (seaweedfs).
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 argparse
import os
import sys
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 (seaweedfs) backend URL", default="localhost:9000")
parser.add_argument(
"--s3-access-key",
help="S3 (seaweedfs) credential",
default=os.environ.get("SANDCRAWLER_BLOB_ACCESS_KEY")
or os.environ.get("MINIO_ACCESS_KEY"),
)
parser.add_argument(
"--s3-secret-key",
help="S3 (seaweedfs) credential",
default=os.environ.get("SANDCRAWLER_BLOB_ACCESS_KEY")
or os.environ.get("MINIO_SECRET_KEY"),
)
parser.add_argument(
"--s3-bucket", help="S3 (seaweedfs) 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 (seaweedfs)"
)
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 (seaweedfs)"
)
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 (seaweedfs)"
)
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()
|
