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Diffstat (limited to 'python/persist_tool.py')
| -rwxr-xr-x | python/persist_tool.py | 311 |
1 files changed, 311 insertions, 0 deletions
diff --git a/python/persist_tool.py b/python/persist_tool.py new file mode 100755 index 0000000..e08d66c --- /dev/null +++ b/python/persist_tool.py @@ -0,0 +1,311 @@ +#!/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 run_crossref(args): + batch_size = 200 + if args.parse_refs: + batch_size = 10 + grobid_client = GrobidClient( + host_url=args.grobid_host, + ) + worker = PersistCrossrefWorker( + db_url=args.db_url, + grobid_client=grobid_client, + parse_refs=args.parse_refs, + ) + pusher = JsonLinePusher( + worker, + args.json_file, + batch_size=batch_size, + ) + pusher.run() + + +def run_grobid_refs(args): + worker = PersistGrobidRefsWorker( + db_url=args.db_url, + ) + pusher = JsonLinePusher( + worker, + args.json_file, + batch_size=100, + ) + 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"), + ) + + sub_crossref = subparsers.add_parser( + "crossref", + help="backfill a crossref JSON dump into postgresql, and extract references at the same time", + ) + sub_crossref.set_defaults(func=run_crossref) + sub_crossref.add_argument( + "json_file", + help="crossref file to import from (or '-' for stdin)", + type=argparse.FileType("r"), + ) + sub_crossref.add_argument( + "--grobid-host", default="https://grobid.qa.fatcat.wiki", help="GROBID API host/port" + ) + sub_crossref.add_argument( + "--parse-refs", + action="store_true", + help="use GROBID to parse any unstructured references (default is to not)", + ) + + sub_grobid_refs = subparsers.add_parser( + "grobid-refs", help="backfill a grobid_refs JSON dump into postgresql" + ) + sub_grobid_refs.set_defaults(func=run_grobid_refs) + sub_grobid_refs.add_argument( + "json_file", + help="grobid_refs 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() |