From a613cf2fa66e59c412b9de15e487ab5d3431bb51 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Mon, 4 Oct 2021 12:56:56 -0700 Subject: old (2020) notes on pdfextract cleanup --- notes/tasks/2020-10-21_pdfextract_holes.md | 74 ++++++++++++++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 notes/tasks/2020-10-21_pdfextract_holes.md diff --git a/notes/tasks/2020-10-21_pdfextract_holes.md b/notes/tasks/2020-10-21_pdfextract_holes.md new file mode 100644 index 0000000..c0bb65e --- /dev/null +++ b/notes/tasks/2020-10-21_pdfextract_holes.md @@ -0,0 +1,74 @@ + +Realized I had not enabled persisting of PDF extraction results (thumbnail, +text) in ingest worker when added over the summer. So now need to run a +catch-up. This applied to both "live" and "bulk" ingest. + +## `cdx` / `ingest` / `grobid` catch-up + +First, re-run extraction for cases where we did an ingest, and grobid ran +successfully, and we have a CDX row, but no `pdf_meta`: + + -- this is a slow query + COPY ( + SELECT DISTINCT ON (cdx.sha1hex) row_to_json(cdx) + FROM grobid + LEFT JOIN cdx ON grobid.sha1hex = cdx.sha1hex + --LEFT JOIN fatcat_file ON grobid.sha1hex = fatcat_file.sha1hex + LEFT JOIN ingest_file_result ON grobid.sha1hex = ingest_file_result.terminal_sha1hex + LEFT JOIN pdf_meta ON grobid.sha1hex = pdf_meta.sha1hex + WHERE cdx.sha1hex IS NOT NULL + --AND fatcat_file.sha1hex IS NOT NULL + AND ingest_file_result.terminal_sha1hex IS NOT NULL + AND pdf_meta.sha1hex IS NULL + ) + TO '/grande/snapshots/dump_unextracted_pdf.ingest.2020-10-21.json' + WITH NULL ''; + => 19,676,116 + +Wow, that is a lot. Many from recent OAI-PMH and OA crawls, presumably. + + cat /grande/snapshots/dump_unextracted_pdf.ingest.2020-10-21.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + +And again, after a couple partitions got hung up: + + COPY ( + SELECT DISTINCT ON (cdx.sha1hex) row_to_json(cdx) + FROM grobid + LEFT JOIN cdx ON grobid.sha1hex = cdx.sha1hex + --LEFT JOIN fatcat_file ON grobid.sha1hex = fatcat_file.sha1hex + LEFT JOIN ingest_file_result ON grobid.sha1hex = ingest_file_result.terminal_sha1hex + LEFT JOIN pdf_meta ON grobid.sha1hex = pdf_meta.sha1hex + WHERE cdx.sha1hex IS NOT NULL + --AND fatcat_file.sha1hex IS NOT NULL + AND ingest_file_result.terminal_sha1hex IS NOT NULL + AND pdf_meta.sha1hex IS NULL + ) + TO '/grande/snapshots/dump_unextracted_pdf.ingest.2020-11-04.json' + WITH NULL ''; + + + cat /grande/snapshots/dump_unextracted_pdf.ingest.2020-11-04.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + => 562k 0:00:16 [34.6k/s] + +## `petabox` / `grobid` catch-up + +These didn't all seem to extract correctly before after 1.5m rows, there will +still 900k unprocessed. Trying again. + + COPY ( + SELECT DISTINCT ON (petabox.sha1hex) row_to_json(petabox) + FROM grobid + LEFT JOIN petabox ON grobid.sha1hex = petabox.sha1hex + LEFT JOIN pdf_meta ON grobid.sha1hex = pdf_meta.sha1hex + WHERE petabox.sha1hex IS NOT NULL + AND pdf_meta.sha1hex IS NULL + ) + TO '/grande/snapshots/dump_unextracted_pdf_petabox.2020-11-04.json' + WITH NULL ''; + + cat /grande/snapshots/dump_unextracted_pdf_petabox.ingest.2020-11-04.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + +## `cdx` / `grobid` catch-up + +Next will be to process PDFs with GROBID and CDX but no ingest. + -- cgit v1.2.3