add notes on recent ingest and backfill tasks

3 files changed, 221 insertions, 0 deletions

diff --git a/notes/tasks/2020-01-06_heuristic_cdx.txt b/notes/tasks/2020-01-06_heuristic_cdx.txt
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+
+Wanted to include a large number of additional CDX lines based on regex
+pattern. These are primarily .edu domains with things that look like user
+accounts *and* .pdf file extensions in the path.
+
+## Commands
+
+aitio:/fast/gwb_pdfs
+
+  pdfs/gwb-pdf-20191005172329-url-heuristics-edu
+  pdfs/gwb-pdf-20191005172329-url-heuristics
+
+
+to filter as url/sha1 uniq:
+
+    cat raw.cdx | sort -u -t' ' -k3,6 -S 4G > uniq.cdx
+
+    cat gwb-pdf-20191005172329-url-heuristics-edu/part-r-000* | sort -u -t' ' -k3,6 -S 4G > gwb-pdf-20191005172329-url-heuristics-edu.uniq_url_sha1.cdx
+    cat gwb-pdf-20191005172329-url-heuristics/part-r-000* | sort -u -t' ' -k3,6 -S 4G > gwb-pdf-20191005172329-url-heuristics.uniq_url_sha1.cdx
+
+    7241795  gwb-pdf-20191005172329-url-heuristics-edu.uniq_url_sha1.cdx
+    41137888 gwb-pdf-20191005172329-url-heuristics.uniq_url_sha1.cdx
+
+    cut -d' ' -f6 gwb-pdf-20191005172329-url-heuristics-edu.uniq_url_sha1.cdx | sort -u -S 4G | wc -l
+    7241795
+
+    cut -d' ' -f6 gwb-pdf-20191005172329-url-heuristics.uniq_url_sha1.cdx | sort -u -S 4G | wc -l
+    41137888
+
+    ./persist_tool.py cdx /fast/gwb_pdf/gwb-pdf-20191005172329-url-heuristics-edu.uniq_url_sha1.cdx
+    Worker: Counter({'total': 7239153, 'insert-cdx': 6845283, 'update-cdx': 0})
+    CDX lines pushed: Counter({'total': 7241795, 'pushed': 7239153, 'skip-parse': 2603, 'skip-mimetype': 39})
+
+    ./persist_tool.py cdx /fast/gwb_pdf/gwb-pdf-20191005172329-url-heuristics.uniq_url_sha1.cdx
+    Worker: Counter({'total': 41030360, 'insert-cdx': 22430064, 'update-cdx': 0})
+    CDX lines pushed: Counter({'total': 41137888, 'pushed': 41030360, 'skip-mimetype': 87341, 'skip-parse': 20187})
+
diff --git a/notes/tasks/2020-01-27_grobid_backfill.md b/notes/tasks/2020-01-27_grobid_backfill.md
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+
+Recently added a bunch of PDFs to sandcrawler-db. Want to GROBID extract the
+~15m which haven't been processed yet. Also want to re-GROBID a batch of
+PDFs-in-zipfiles from archive.org; will probably also want to re-GROBID other
+petabox files soon.
+
+## pre-1923 zipfile re-extraction
+
+Exact commands (in parallel):
+
+    fd .zip /srv/sandcrawler/tasks/crossref-pre-1909-scholarly-works/ | \
+            parallel -j16 --progress --joblog extract_tasks.log --resume-failed \
+            './grobid_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --grobid-host http://localhost:8070 extract-zipfile {}'
+
+    fd .zip /srv/sandcrawler/tasks/crossref-pre-1923-scholarly-works/ | \
+            parallel -j16 --progress --joblog extract_tasks_1923.log --resume-failed \
+            './grobid_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --grobid-host http://localhost:8070 extract-zipfile {}'
+
+## petabox re-extraction
+
+This was run around 2020-02-03. There are a few million remaining PDFs that
+have only partial file metadata (`file_meta`), meaning run with old version of
+sandcrawler code. Want to get them all covered, maybe even DELETE the missing
+ones, so re-grobiding petabox-only files.
+
+There are about 2,887,834 files in petabox, only 46,232 need re-processing (!).
+
+    psql sandcrawler < dump_regrobid_pdf_petabox.sql
+    cat dump_regrobid_pdf_petabox.2020-02-03.json | sort -S 4G | uniq -w 40 | cut -f2 > dump_regrobid_pdf_petabox.2020-02-03.uniq.json
+
+This is pretty few... maybe even would have been caught by wayback backfill?
+
+Small start:
+
+    head /srv/sandcrawler/tasks/dump_regrobid_pdf_petabox.2020-02-03.uniq.json | ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json -
+
+Full batch, 25x parallel:
+
+    cat /srv/sandcrawler/tasks/dump_regrobid_pdf_petabox.2020-02-03.uniq.json | pv -l | parallel -j25 --pipe ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json -
+
diff --git a/notes/tasks/2020-02-04_ingest_backfills.md b/notes/tasks/2020-02-04_ingest_backfills.md
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+
+
+## Using Fatcat Tool
+
+Want to enqueue some backfill URLs to crawl, now that SPNv2 is on the mend.
+
+Example dry-run:
+
+    ./fatcat_ingest.py --dry-run --limit 50 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --name elife
+
+Big OA from 2020 (past month):
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --name elife
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 158 release objects in search queries
+    Counter({'ingest_request': 158, 'estimate': 158, 'kafka': 158, 'elasticsearch_release': 158})
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --name elife
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 2312 release objects in search queries
+    Counter({'kafka': 2312, 'ingest_request': 2312, 'elasticsearch_release': 2312, 'estimate': 2312})
+
+    # note: did 100 first to test
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --name plos
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 1185 release objects in search queries
+    Counter({'estimate': 1185, 'ingest_request': 1185, 'elasticsearch_release': 1185, 'kafka': 1185})
+
+    ./fatcat_ingest.py --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher elsevier
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 89 release objects in search queries
+    Counter({'elasticsearch_release': 89, 'estimate': 89, 'ingest_request': 89, 'kafka': 89})
+
+    ./fatcat_ingest.py --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher ieee
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 499 release objects in search queries
+    Counter({'kafka': 499, 'ingest_request': 499, 'estimate': 499, 'elasticsearch_release': 499})
+
+    ./fatcat_ingest.py --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --name bmj
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 28 release objects in search queries
+    Counter({'elasticsearch_release': 28, 'ingest_request': 28, 'kafka': 28, 'estimate': 28})
+
+    ./fatcat_ingest.py --dry-run --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher springer
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 6225 release objects in search queries
+    Counter({'estimate': 6225, 'kafka': 500, 'elasticsearch_release': 500, 'ingest_request': 500})
+
+    ./fatcat_ingest.py --limit 1000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 2920 release objects in search queries
+    Counter({'estimate': 2920, 'elasticsearch_release': 1001, 'ingest_request': 1000, 'kafka': 1000})
+
+Hip corona virus papers:
+
+    ./fatcat_ingest.py --limit 2000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query coronavirus
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 5332 release objects in search queries
+    Counter({'estimate': 5332, 'elasticsearch_release': 2159, 'ingest_request': 2000, 'kafka': 2000})
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query 2019-nCoV
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 110 release objects in search queries
+    Counter({'ingest_request': 110, 'kafka': 110, 'elasticsearch_release': 110, 'estimate': 110})
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query MERS-CoV
+    Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests
+    Expecting 589 release objects in search queries
+    Counter({'estimate': 589, 'elasticsearch_release': 589, 'ingest_request': 552, 'kafka': 552})
+
+
+Mixed eLife results:
+
+    ["wrong-mimetype",null,"https://elifesciences.org/articles/54551"]
+    ["success",null,"https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNTE2OTEvZWxpZmUtNTE2OTEtdjEucGRm/elife-51691-v1.pdf?_hash=Jp1cLog1NzIlU%2BvjgLdbM%2BuphOwe5QWUn%2F97tbQBNG4%3D"]
+
+## Re-Request Failed
+
+Select some failed injest request rows to re-enqueue:
+
+    COPY (
+        SELECT row_to_json(ingest_request.*) FROM ingest_request
+        LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url
+        WHERE ingest_request.ingest_type = 'pdf'
+            AND ingest_file_result.ingest_type = 'pdf'
+            AND ingest_file_result.updated < NOW() - '2 day'::INTERVAL
+            AND ingest_file_result.hit = false
+            AND ingest_file_result.status = 'spn2-cdx-lookup-failure'
+    ) TO '/grande/snapshots/reingest_spn2cdx_20200205.rows.json';
+    -- 1536 rows
+
+Transform back to full requests:
+
+    ./scripts/ingestrequest_row2json.py reingest_spn2cdx_20200205.rows.json > reingest_spn2cdx_20200205.json
+
+Push into kafka (on a kafka broker node):
+
+    cat ~/reingest_spn2cdx_20200205.json | jq . -c | kafkacat -P -b localhost -t sandcrawler-prod.ingest-file-requests -p -1
+
+More:
+
+    COPY (
+        SELECT row_to_json(ingest_request.*) FROM ingest_request
+        LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url
+        WHERE ingest_request.ingest_type = 'pdf'
+            AND ingest_file_result.ingest_type = 'pdf'
+            AND ingest_file_result.updated < NOW() - '2 day'::INTERVAL
+            AND ingest_file_result.hit = false
+            AND ingest_file_result.status like 'error:%'
+    ) TO '/grande/snapshots/reingest_spn2err1_20200205.rows.json';
+    -- COPY 1516
+
+    COPY (
+        SELECT row_to_json(ingest_request.*) FROM ingest_request
+        LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url
+        WHERE ingest_request.ingest_type = 'pdf'
+            AND ingest_file_result.ingest_type = 'pdf'
+            AND ingest_file_result.updated < NOW() - '2 day'::INTERVAL
+            AND ingest_file_result.hit = false
+            AND ingest_file_result.status like 'spn2-error%'
+    ) TO '/grande/snapshots/reingest_spn2err2_20200205.rows.json';
+    -- COPY 16678
+
+The next large ones to try would be `wayback-error` and `cdx-error`, though
+these are pretty generic. Could go kafka output to try and understand those
+error classes better.
+
+Oof, as a mistake enqueued to partition 1 instead of -1 (random), so these will
+take a week or more to actually process. Re-enqueued as -1; ingesting from
+wayback is pretty fast, this should result mostly wayback ingests. Caught up by
+end of weekend?
+
+## Check Coverages
+
+As follow-ups:
+
+    elife: https://fatcat.wiki/container/en4qj5ijrbf5djxx7p5zzpjyoq/coverage
+    archivist: https://fatcat.wiki/container/zpobyv4vbranllc7oob56tgci4/coverage
+        => 85 preserved
+    jcancer: https://fatcat.wiki/container/nkkzpwht7jd3zdftc6gq4eoeey/coverage
+        => 2020 preserved
+        => 2520 preserved
+    plos: https://fatcat.wiki/container/23nqq3odsjhmbi5tqavvcn7cfm/coverage
+