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diff --git a/notes/ingest/2020-05_oai_pmh.md b/notes/ingest/2020-05_oai_pmh.md new file mode 100644 index 0000000..4cfd8d5 --- /dev/null +++ b/notes/ingest/2020-05_oai_pmh.md @@ -0,0 +1,125 @@ + +Primary Goal: start large crawl of OAI landing pages that we haven't seen + +Fields of interest for ingest: +- oai identifer +- doi +- formats +- urls (maybe also "relations") +- types (type+stage) + +## Other Tasks + +About 150 million total lines. + +Types coverage + + zstdcat oai.ndjson.zst | pv -l | jq "select(.types != null) | .types[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > types_counts.txt + +Dump all ISSNs, with counts, quick check how many are in chocula/fatcat + + zstdcat oai.ndjson.zst | pv -l | jq "select(.issn != null) | .issn[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > issn_counts.txt + +Language coverage + + zstdcat oai.ndjson.zst | pv -l | jq "select(.languages != null) | .languages[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > languages_counts.txt + +Format coverage + + zstdcat oai.ndjson.zst | pv -l | jq "select(.formats != null) | .formats[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > formats_counts.txt + => 150M 0:56:14 [44.7k/s] + +Have a DOI? + + zstdcat oai.ndjson.zst | pv -l | rg '"doi":' | rg '"10.' | wc -l + => 16,013,503 + + zstdcat oai.ndjson.zst | pv -l | jq "select(.doi != null) | .doi[]" -r | sort -u -S 5G > doi_raw.txt + => 11,940,950 + +## Transform, Load, Bulk Ingest + + zstdcat oai.ndjson.zst | ./oai2ingestrequest.py - | pv -l | gzip > oai.202002.requests.json.gz + => 80M 6:36:55 [3.36k/s] + + time zcat /schnell/oai-pmh/oai.202002.requests.json.gz | pv -l | ./persist_tool.py ingest-request - + => 80M 4:00:21 [5.55k/s] + => Worker: Counter({'total': 80013963, 'insert-requests': 51169081, 'update-requests': 0}) + => JSON lines pushed: Counter({'pushed': 80013963, 'total': 80013963}) + + => real 240m21.207s + => user 85m12.576s + => sys 3m29.580s + + select count(*) from ingest_request where ingest_type = 'pdf' and link_source = 'oai'; + => 51,185,088 + +Why so many (30 million) skipped? Not unique? + + zcat oai.202002.requests.json.gz | jq '[.link_source_id, .base_url]' -c | sort -u -S 4G | wc -l + => 51,185,088 + + zcat oai.202002.requests.json.gz | jq .base_url -r | pv -l | sort -u -S 4G > request_url.txt + wc -l request_url.txt + => 50,002,674 request_url.txt + + zcat oai.202002.requests.json.gz | jq .link_source_id -r | pv -l | sort -u -S 4G > requires_oai.txt + wc -l requires_oai.txt + => 34,622,083 requires_oai.txt + +Yup, tons of duplication. And remember this is exact URL, not SURT or similar. + +How many of these are URLs we have seen and ingested already? + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + | 49491452 + success | 1469113 + no-capture | 134611 + redirect-loop | 59666 + no-pdf-link | 8947 + cdx-error | 7561 + terminal-bad-status | 6704 + null-body | 5042 + wrong-mimetype | 879 + wayback-error | 722 + petabox-error | 198 + gateway-timeout | 86 + link-loop | 51 + invalid-host-resolution | 24 + spn2-cdx-lookup-failure | 22 + spn2-error | 4 + bad-gzip-encoding | 4 + spn2-error:job-failed | 2 + (18 rows) + +Dump ingest requests: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND date(ingest_request.created) > '2020-05-01' + AND ingest_file_result.status IS NULL + ) TO '/grande/snapshots/oai_noingest_20200506.requests.json'; + => COPY 49491452 + + cat /grande/snapshots/oai_noingest_20200506.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + |