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Diffstat (limited to 'notes/tasks')
| -rw-r--r-- | notes/tasks/2020-02-04_ingest_backfills.md | 148 | ||||
| -rw-r--r-- | notes/tasks/2020-02-18_ingest_backfills.md | 42 | ||||
| -rw-r--r-- | notes/tasks/2020-02-21_ingest_backfills.md | 104 |
3 files changed, 0 insertions, 294 deletions
diff --git a/notes/tasks/2020-02-04_ingest_backfills.md b/notes/tasks/2020-02-04_ingest_backfills.md deleted file mode 100644 index 73a42ef..0000000 --- a/notes/tasks/2020-02-04_ingest_backfills.md +++ /dev/null @@ -1,148 +0,0 @@ - - -## 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 - => 2020-02-24: 7187 / 8101 = 88% preserved - archivist: https://fatcat.wiki/container/zpobyv4vbranllc7oob56tgci4/coverage - => 85 preserved - => 2020-02-24: 85 / 3005 preserved (TODO) - jcancer: https://fatcat.wiki/container/nkkzpwht7jd3zdftc6gq4eoeey/coverage - => 2020 preserved - => 2520 preserved - => 2020-02-24: 2700 / 2766 preserved - plos: https://fatcat.wiki/container/23nqq3odsjhmbi5tqavvcn7cfm/coverage - => 2020-02-24: 7580 / 7730 = 98% preserved - diff --git a/notes/tasks/2020-02-18_ingest_backfills.md b/notes/tasks/2020-02-18_ingest_backfills.md deleted file mode 100644 index 1ab18f4..0000000 --- a/notes/tasks/2020-02-18_ingest_backfills.md +++ /dev/null @@ -1,42 +0,0 @@ - -Select: - - 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_spn2err_20200218.rows.json'; - => COPY 6537 - - 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.hit = false - AND ingest_file_result.status like 'wayback-error' - ) TO '/grande/snapshots/reingest_waybackerr_20200218.rows.json'; - => COPY 33022 - -Transform: - - ./scripts/ingestrequest_row2json.py reingest_spn2err_20200218.rows.json > reingest_spn2err_20200218.json - ./scripts/ingestrequest_row2json.py reingest_waybackerr_20200218.rows.json > reingest_waybackerr_20200218.json - -Push to kafka: - - cat reingest_spn2err_20200218.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 - cat reingest_waybackerr_20200218.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 - -Many had null `ingest_request_source`, so won't actually import into fatcat: - - bnewbold@ia601101$ cat reingest_waybackerr_20200218.json | jq .ingest_request_source | sort | uniq -c | sort -n - 1 "savepapernow-web" - 112 "fatcat-ingest-container" - 11750 "fatcat-changelog" - 21159 null - diff --git a/notes/tasks/2020-02-21_ingest_backfills.md b/notes/tasks/2020-02-21_ingest_backfills.md deleted file mode 100644 index 48df910..0000000 --- a/notes/tasks/2020-02-21_ingest_backfills.md +++ /dev/null @@ -1,104 +0,0 @@ - -Follow-ups to last ingest backfill. Only run these when ingest request topic is -empty, and full persist chain has run successfully. - -## Corona virus stuff - - ./fatcat_ingest.py --limit 2000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query coronavirus - - ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query 2019-nCoV - - ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query MERS-CoV - -## Large OA Publishers - -Should probably check domain stats/success for all of these first. - -Would also be good to have a "randomize" option. Could fake that by dumping to -disk first. - - ./fatcat_ingest.py --limit 2000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher elsevier - - ./fatcat_ingest.py --dry-run --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher springer - - # ??? - ./fatcat_ingest.py --limit 1000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4 - -## Fixed OA Publishers (small tests) - - # american archivist - ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4 - => Expecting 2920 release objects in search queries - => Counter({'estimate': 2920, 'elasticsearch_release': 26, 'ingest_request': 25, 'kafka': 25}) - => good - - ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher Gruyter - => Expecting 42897 release objects in search queries - => Counter({'estimate': 42897, 'ingest_request': 25, 'kafka': 25, 'elasticsearch_release': 25}) - - ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher frontiers - => Expecting 35427 release objects in search queries - => Counter({'estimate': 35427, 'kafka': 25, 'elasticsearch_release': 25, 'ingest_request': 25}) - => mixed results? - - ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher mdpi - => Expecting 43111 release objects in search queries - => Counter({'estimate': 43111, 'elasticsearch_release': 25, 'ingest_request': 25, 'kafka': 25}) - => success, fast - - ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher "American Heart Association" - => Expecting 185240 release objects in search queries - => Counter({'estimate': 185240, 'kafka': 25, 'ingest_request': 25, 'elasticsearch_release': 25}) - => no success? or mixed? skip for now - - # Environmental Health Perspectives (NIH) - ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --container-id 3w6amv3ecja7fa3ext35ndpiky - => ["no-pdf-link",null,"https://ehp.niehs.nih.gov/doi/10.1289/ehp.113-a51"] - => ["no-pdf-link",null,"https://ehp.niehs.nih.gov/doi/10.1289/ehp.113-a51"] - => FIXED - => good (but slow?) - - ./fatcat_ingest.py --limit 50 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher "Tomsk State University" - => Expecting 578057 release objects in search queries - => Counter({'estimate': 578057, 'elasticsearch_release': 50, 'kafka': 50, 'ingest_request': 50}) - => nothing from tsu.ru? skip for now - - ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --name "cogent" - => Expecting 4602 release objects in search queries - => Counter({'estimate': 4602, 'kafka': 25, 'elasticsearch_release': 25, 'ingest_request': 25}) - => good - - ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi:10.26434\/chemrxiv*" - => Expecting 5690 release objects in search queries - => Counter({'estimate': 5690, 'ingest_request': 25, 'kafka': 25, 'elasticsearch_release': 25}) - => good - - -## Fixed OA Publishers (full runs) - - # american archivist - ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4 - Expecting 2920 release objects in search queries - Counter({'estimate': 2920, 'elasticsearch_release': 2920, 'kafka': 2911, 'ingest_request': 2911}) - - ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher Gruyter - Expecting 42986 release objects in search queries - Counter({'estimate': 42986, 'elasticsearch_release': 42986, 'kafka': 42935, 'ingest_request': 42935}) - - ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher mdpi - Expecting 43108 release objects in search queries - Counter({'estimate': 43108, 'elasticsearch_release': 43108, 'ingest_request': 41262, 'kafka': 41262}) - - # Environmental Health Perspectives (NIH) - ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --container-id 3w6amv3ecja7fa3ext35ndpiky - Expecting 12699 release objects in search queries - Counter({'elasticsearch_release': 12699, 'estimate': 12699, 'kafka': 12615, 'ingest_request': 12615}) - - ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --name "cogent" - Expecting 4602 release objects in search queries - Counter({'estimate': 4602, 'ingest_request': 4602, 'kafka': 4602, 'elasticsearch_release': 4602}) - - ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi:10.26434\/chemrxiv*" - Expecting 5690 release objects in search queries - Counter({'ingest_request': 5690, 'kafka': 5690, 'estimate': 5690, 'elasticsearch_release': 5690}) - |