diff options
Diffstat (limited to 'notes/cleanups')
| -rw-r--r-- | notes/cleanups/case_sensitive_dois.md | 71 | ||||
| -rw-r--r-- | notes/cleanups/container_issnl_dedupe.md | 105 | ||||
| -rw-r--r-- | notes/cleanups/double_slash_dois.md | 46 | ||||
| -rw-r--r-- | notes/cleanups/file_meta.md | 152 | ||||
| -rw-r--r-- | notes/cleanups/file_release_ingest_bug.md | 192 | ||||
| -rw-r--r-- | notes/cleanups/file_sha1_dedupe.md | 64 | ||||
| -rwxr-xr-x | notes/cleanups/scripts/container_dupe_to_json.py | 55 | ||||
| -rw-r--r-- | notes/cleanups/scripts/fetch_full_cdx_ts.py | 201 | ||||
| -rwxr-xr-x | notes/cleanups/scripts/file2ingestrequest.py | 44 | ||||
| -rwxr-xr-x | notes/cleanups/scripts/file_dupe_to_json.py | 72 | ||||
| -rw-r--r-- | notes/cleanups/wayback_timestamps.md | 304 |
11 files changed, 0 insertions, 1306 deletions
diff --git a/notes/cleanups/case_sensitive_dois.md b/notes/cleanups/case_sensitive_dois.md deleted file mode 100644 index 1bf1901e..00000000 --- a/notes/cleanups/case_sensitive_dois.md +++ /dev/null @@ -1,71 +0,0 @@ - -Relevant github issue: https://github.com/internetarchive/fatcat/issues/83 - -How many existing fatcat releases have a non-lowercase DOI? As of June 2021: - - zcat release_extid.tsv.gz | cut -f3 | rg '[A-Z]' | pv -l | wc -l - 139964 - -## Prep - - wget https://archive.org/download/fatcat_bulk_exports_2021-11-05/release_extid.tsv.gz - - # scratch:bin/fcid.py is roughly the same as `fatcat_util.py uuid2fcid` - - zcat release_extid.tsv.gz \ - | cut -f1,3 \ - | rg '[A-Z]' \ - | /fast/scratch/bin/fcid.py \ - | pv -l \ - > nonlowercase_doi_releases.tsv - # 140k 0:03:54 [ 599 /s] - - wc -l nonlowercase_doi_releases.tsv - 140530 nonlowercase_doi_releases.tsv - -Uhoh, there are ~500 more than previously? Guess those are from after the fix? - -Create a sample for testing: - - shuf -n10000 nonlowercase_doi_releases.tsv \ - > nonlowercase_doi_releases.10k_sample.tsv - -## Test in QA - -In pipenv: - - export FATCAT_AUTH_WORKER_CLEANUP=[...] - - head -n100 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \ - | python -m fatcat_tools.cleanups.release_lowercase_doi - - # Counter({'total': 100, 'update': 100, 'skip': 0, 'insert': 0, 'exists': 0}) - - head -n100 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \ - | python -m fatcat_tools.cleanups.release_lowercase_doi - - # Counter({'total': 100, 'skip-existing-doi-fine': 100, 'skip': 0, 'insert': 0, 'update': 0, 'exists': 0}) - - head -n2000 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \ - | python -m fatcat_tools.cleanups.release_lowercase_doi - - # no such release_ident found: dcjsybvqanffhmu4dhzdnptave - -Presumably because this is being run in QA, and there are some newer prod releases in the snapshot. - -Did a quick update, and then: - - head -n2000 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \ - | python -m fatcat_tools.cleanups.release_lowercase_doi - - # Counter({'total': 2000, 'skip-existing-doi-fine': 1100, 'update': 898, 'skip-existing-not-found': 2, 'skip': 0, 'insert': 0, 'exists': 0}) - -Did some spot checking in QA. Out of 20 DOIs checked, 15 were valid, 5 were not -valid (doi.org 404). It seems like roughly 1/3 have a dupe DOI (the lower-case -DOI exists); didn't count exact numbers. - -This cleanup is simple and looks good to go. Batch size of 50 is good for full -releases. - -Example of parallelization: - - cat /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \ - | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.release_lowercase_doi - - -Ready to go! diff --git a/notes/cleanups/container_issnl_dedupe.md b/notes/cleanups/container_issnl_dedupe.md deleted file mode 100644 index a76bc961..00000000 --- a/notes/cleanups/container_issnl_dedupe.md +++ /dev/null @@ -1,105 +0,0 @@ - -Simply de-duplicating container entities on the basis of ISSN-L. - -Initial plan is to: - -- only merge containers with zero (0) release entities pointing at them -- not update any containers which have had human edits -- not merge additional metadata from redirected entities to the "primary" entity - - -## Prep - -Using commands from `check_issnl.sh`: - - zcat container_export.json.gz \ - | jq '[.issnl, .ident] | @tsv' -r \ - | sort -S 4G \ - | uniq -D -w 9 \ - > issnl_ident.dupes.tsv - - wc -l issnl_ident.dupes.tsv - # 3174 issnl_ident.dupes.tsv - - cut -f1 issnl_ident.dupes.tsv | uniq | wc -l - # 835 - -Run transform script: - - cat issnl_ident.dupes.tsv | ./container_dupe_to_json.py | pv -l > container_issnl_dupes.json - -Create a small random sample: - - shuf -n100 container_issnl_dupes.json > container_issnl_dupes.sample.json - -## QA Testing - - git log | head -n1 - # commit e72d61e60c43911b6d77c4842951441235561dcf - - export FATCAT_AUTH_API_TOKEN=[...] - - head -n25 /srv/fatcat/datasets/container_issnl_dupes.sample.json \ - | python -m fatcat_tools.mergers.containers --editgroup-description-override "Automated merging of duplicate container entities with the same ISSN-L" --dry-run merge-containers - - -Got various errors and patched them: - - AttributeError: 'EntityHistoryEntry' object has no attribute 'editor' - - requests.exceptions.HTTPError: 404 Client Error: NOT FOUND for url: https://fatcat.wiki/container/%7Bident%7D/stats.json - - fatcat_openapi_client.exceptions.ApiValueError: Missing the required parameter `editgroup_id` when calling `accept_editgroup` - -Run again: - - head -n25 /srv/fatcat/datasets/container_issnl_dupes.sample.json \ - | python -m fatcat_tools.mergers.containers --editgroup-description-override "Automated merging of duplicate container entities with the same ISSN-L" --dry-run merge-containers - - # Running in dry-run mode! - # Counter({'updated-entities': 96, 'skip-container-release-count': 84, 'lines': 25, 'merged': 25, 'skip': 0, 'updated-total': 0}) - -Finally! dry-run mode actually worked. Try entire sample in dry-run: - - cat /srv/fatcat/datasets/container_issnl_dupes.sample.json \ - | python -m fatcat_tools.mergers.containers --editgroup-description-override "Automated merging of duplicate container entities with the same ISSN-L" --dry-run merge-containers - - # Running in dry-run mode! - # Counter({'updated-entities': 310, 'skip-container-release-count': 251, 'lines': 100, 'merged': 100, 'skip': 0, 'updated-total': 0}) - -How about a small `max-container-releases`: - - cat /srv/fatcat/datasets/container_issnl_dupes.sample.json \ - | python -m fatcat_tools.mergers.containers --editgroup-description-override "Automated merging of duplicate container entities with the same ISSN-L" --dry-run merge-containers - - # Running in dry-run mode! - # Counter({'updated-entities': 310, 'skip-container-release-count': 251, 'lines': 100, 'merged': 100, 'skip': 0, 'updated-total': 0}) - -Exact same count... maybe something isn't working? Debugged and fixed it. - - requests.exceptions.HTTPError: 503 Server Error: SERVICE UNAVAILABLE for url: https://fatcat.wiki/container/xn7i2sdijzbypcetz77kttj76y/stats.json - - # Running in dry-run mode! - # Counter({'updated-entities': 310, 'lines': 100, 'merged': 100, 'skip-container-release-count': 92, 'skip': 0, 'updated-total': 0}) - -From skimming, it looks like 100 is probably a good cut-off. There are sort of -a lot of these dupes! - -Try some actual merges: - - head -n25 /srv/fatcat/datasets/container_issnl_dupes.sample.json \ - | python -m fatcat_tools.mergers.containers --editgroup-description-override "Automated merging of duplicate container entities with the same ISSN-L" merge-containers - - # Counter({'updated-entities': 96, 'skip-container-release-count': 84, 'lines': 25, 'merged': 25, 'skip': 0, 'updated-total': 0}) - -Run immediately again: - - # Counter({'lines': 25, 'skip': 25, 'skip-not-active-entity': 25, 'skip-container-release-count': 2, 'merged': 0, 'updated-total': 0}) - -Run all the samples, with limit of 100 releases: - - cat /srv/fatcat/datasets/container_issnl_dupes.sample.json \ - | python -m fatcat_tools.mergers.containers --editgroup-description-override "Automated merging of duplicate container entities with the same ISSN-L" merge-containers - --max-container-releases 100 - # Counter({'updated-entities': 214, 'lines': 100, 'merged': 75, 'skip': 25, 'skip-not-active-entity': 25, 'skip-container-release-count': 15, 'updated-total': 0}) - -Wow, there are going to be a lot of these containers not merged because they -have so many releases! Will have to do a second, more carefully reviewed (?) -round of merging. - -Unfortunately, not seeing any human-edited container entities here to check if -that filter is working. diff --git a/notes/cleanups/double_slash_dois.md b/notes/cleanups/double_slash_dois.md deleted file mode 100644 index d4e9ded6..00000000 --- a/notes/cleanups/double_slash_dois.md +++ /dev/null @@ -1,46 +0,0 @@ - -Relevant github issue: https://github.com/internetarchive/fatcat/issues/48 - - -## Investigate - -At least some of these DOIs actually seem valid, like -`10.1026//1616-1041.3.2.86`. So shouldn't be re-writing them! - - zcat release_extid.tsv.gz \ - | cut -f1,3 \ - | rg '\t10\.\d+//' \ - | wc -l - # 59,904 - - zcat release_extid.tsv.gz \ - | cut -f1,3 \ - | rg '\t10\.\d+//' \ - | pv -l \ - > doubleslash_dois.tsv - -Which prefixes have the most double slashes? - - cat doubleslash_dois.tsv | cut -f2 | cut -d/ -f1 | sort | uniq -c | sort -nr | head - 51220 10.1037 - 2187 10.1026 - 1316 10.1024 - 826 10.1027 - 823 10.14505 - 443 10.17010 - 186 10.46925 - 163 10.37473 - 122 10.18376 - 118 10.29392 - [...] - -All of the 10.1037 DOIs seem to be registered with Crossref, and at least some -have redirects to the not-with-double-slash versions. Not all doi.org lookups -include a redirect. - -I think the "correct thing to do" here is to add special-case handling for the -pubmed and crossref importers, and in any other case allow double slashes. - -Not clear that there are any specific cleanups to be done for now. A broader -"verify that DOIs are actually valid" push and cleanup would make sense; if -that happens checking for mangled double-slash DOIs would make sense. diff --git a/notes/cleanups/file_meta.md b/notes/cleanups/file_meta.md deleted file mode 100644 index d99e821e..00000000 --- a/notes/cleanups/file_meta.md +++ /dev/null @@ -1,152 +0,0 @@ - -Over 500k file entities still lack complete metadata. For example, SHA-256 -checksums and verified mimetypes. - -Presumably these also lack GROBID processing. It seems that most or all of -these are simply wayback captures with no CDX metadata in sandcrawler-db, so -they didn't get update in prior cleanups. - -Current plan, re-using existing tools and processes, is to: - -1. create stub ingest requests containing file idents -2. process them "locally" on a large VM, in 'bulk' mode; writing output to stdout but using regular grobid and pdfextract "sinks" to Kafka -3. transform ingest results to a form for existing `file_meta` importer -4. run imports - -The `file_meta` importer requires just the `file_meta` dict from sandcrawler. - -## Prep - - zcat file_hashes.tsv.gz | pv -l | rg '\t\t' | wc -l - # 521,553 - - zcat file_export.json.gz \ - | rg -v '"sha256":' \ - | pv -l \ - | pigz \ - > files_missing_sha256.json.gz - # 521k 0:10:21 [ 839 /s] - -Want ingest requests with: - - base_url: str - ingest_type: "pdf" - link_source: "fatcat" - link_source_id: file ident (with "file_" prefix) - ingest_request_source: "file-backfill" - ext_ids: - sha1: str - -Use `file2ingestrequest.py` helper: - - zcat files_missing_sha256.json.gz \ - | ./file2ingestrequest.py \ - | pv -l \ - | pigz \ - > files_missing_sha256.ingest_request.json.gz - # 519k 0:00:19 [26.5k/s] - -So about 2k filtered out, will investigate later. - - zcat files_missing_sha256.ingest_request.json.gz \ - | shuf -n1000 \ - > files_missing_sha256.ingest_request.sample.json - - head -n100 files_missing_sha256.ingest_request.sample.json | ./ingest_tool.py requests --no-spn2 - > sample_results.json - 4 "no-capture" - 1 "no-pdf-link" - 95 "success" - -Seems like this is going to be a good start, but will need iteration. - -Dev testing: - - head files_missing_sha256.ingest_request.sample.json \ - | ./ingest_tool.py file-requests-backfill - --kafka-env qa --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 \ - > out_sample.json - - -## Commands - -Production warm-up: - - cat /srv/sandcrawler/tasks/files_missing_sha256.ingest_request.sample.json \ - | ./ingest_tool.py file-requests-backfill - --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 \ - > /srv/sandcrawler/tasks/files_missing_sha256.ingest_results.sample.json - -Production parallel run: - - zcat /srv/sandcrawler/tasks/files_missing_sha256.ingest_request.json \ - | parallel -j24 --linebuffer --round-robin --pipe ./ingest_tool.py file-requests-backfill - --kafka-env qa --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 \ - > /srv/sandcrawler/tasks/files_missing_sha256.ingest_results.json - -Filter and select file meta for import: - - head files_missing_sha256.ingest_results.json \ - | rg '"sha256hex"' \ - | jq 'select(.request.ext_ids.sha1 == .file_meta.sha1hex) | .file_meta' -c \ - > files_missing_sha256.file_meta.json - # Worker: Counter({'total': 20925, 'success': 20003, 'no-capture': 545, 'link-loop': 115, 'wrong-mimetype': 104, 'redirect-loop': 46, 'wayback-error': 25, 'null-body': 20, 'no-pdf-link': 18, 'skip-url-blocklist': 17, 'terminal-bad-status': 16, 'cdx-error': 9, 'wayback-content-error': 4, 'blocked-cookie': 3}) - # [etc] - - -Had some GROBID issues, so are not going to be able to get everything in first -pass. Merge our partial results, as just `file_meta`: - - cat files_missing_sha256.ingest_results.batch1.json files_missing_sha256.ingest_results.json \ - | jq .file_meta -c \ - | rg '"sha256hex"' \ - | pv -l \ - > files_missing_sha256.file_meta.json - # 386k 0:00:41 [9.34k/s] - -A bunch of these will need to be re-run once GROBID is in a healthier place. - -Check that we don't have (many) dupes: - - cat files_missing_sha256.file_meta.json \ - | jq .sha1hex -r \ - | sort \ - | uniq -D \ - | wc -l - # 86520 - -Huh, seems like a weirdly large number. Maybe related to re-crawling? Will need -to dedupe by sha1hex. - -Check how many dupes in original: - - zcat files_missing_sha256.ingest_request.json.gz | jq .ext_ids.sha1 -r | sort | uniq -D | wc -l - -That lines up with dupes expected before SHA-1 de-dupe run. - - cat files_missing_sha256.file_meta.json \ - | sort -u -S 4G \ - | pv -l \ - > files_missing_sha256.file_meta.uniq.json - - cat files_missing_sha256.file_meta.uniq.json \ - | jq .sha1hex -r \ - | sort \ - | uniq -D \ - | wc -l - # 0 - -Have seen a lot of errors like: - - %4|1637808915.562|TERMINATE|rdkafka#producer-1| [thrd:app]: Producer terminating with 1 message (650 bytes) still in queue or transit: use flush() to wait for outstanding message delivery - -TODO: add manual `finish()` calls on sinks in tool `run` function - -## QA Testing - - export FATCAT_API_AUTH_TOKEN... # sandcrawler-bot - - cat /srv/fatcat/datasets/files_missing_sha256.file_meta.uniq.sample.json \ - | ./fatcat_import.py --editgroup-description-override 'backfill of full file-level metadata for early-imported papers' file-meta - - # Counter({'total': 1000, 'update': 503, 'skip-existing-complete': 403, 'skip-no-match': 94, 'skip': 0, 'insert': 0, 'exists': 0}) - - head -n1000 /srv/fatcat/datasets/files_missing_sha256.file_meta.uniq.json \ - | parallel -j8 --round-robin --pipe -q ./fatcat_import.py --editgroup-description-override 'backfill of full file-level metadata for early-imported papers' file-meta - - # Counter({'total': 1000, 'update': 481, 'skip-existing-complete': 415, 'skip-no-match': 104, 'skip': 0, 'insert': 0, 'exists': 0}) - diff --git a/notes/cleanups/file_release_ingest_bug.md b/notes/cleanups/file_release_ingest_bug.md deleted file mode 100644 index d818905b..00000000 --- a/notes/cleanups/file_release_ingest_bug.md +++ /dev/null @@ -1,192 +0,0 @@ - -We want to find cases where the `file_edit` metadata for a file entity does not match the DOI of the release it is linked to. - -## Background - - -Seems to mostly happen when the `link_source_id` DOI is not found during a -fatcat 'lookup', eg due to upstream DOI metadata not including a 'title' field -(required by fatcat schema). Many of these seem to be 'journal-issue' or -something like that. Presumably upstream (unpaywall) crawled and found some PDF -for the DOI and indexes that. - -TODO: what was the specific code bug that caused this? time window of edits? -https://github.com/internetarchive/fatcat/commit/d8cf02dbdc6848be4de2710e54f4463d702b6e7c - -TODO: how many empty-title Crossref DOIs are there? perhaps we should import these after all, in some situations? eg, pull `html_biblio`? -TODO: examples of other mismatches? edits from the same timespan with mismatching identifiers - -## Queries - - file_edit - ident_id - rev_id - extra_json->>'link_source_id'::text - file_rev_release - file_rev - target_release_ident_id - release_ident - id - rev_id - release_rev - id - doi - -Query some samples: - - SELECT file_edit.ident_id as file_ident, release_ident.id as release_ident, file_edit.extra_json->>'link_source_id' as file_edit_doi, release_rev.doi as release_doi - FROM file_edit - LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev - LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id - LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id - WHERE - file_edit.extra_json->>'ingest_request_source' = 'unpaywall' - AND release_rev.doi != file_edit.extra_json->>'link_source_id' - LIMIT 20; - - file_ident | release_ident | file_edit_doi | release_doi - --------------------------------------+--------------------------------------+---------------------------------------+------------------------------------- - 8fe6eb2a-da3a-4e1c-b281-85fad3cae601 | 0a0cbabd-3f04-4296-94d5-b61c27fddee4 | 10.7167/2013/520930/dataset/3 | 10.7167/2013/520930 - cbb2d4e7-a9a7-41df-be1d-faf9dd552ee1 | d7b356c7-de6b-4885-b37d-ea603849a30a | 10.1525/elementa.124.t1 | 10.1525/elementa.124 - 26242648-2a7b-42ea-b2ca-e4fba8f0a2c7 | d2647e07-fbb3-47f5-b06a-de2872bf84ec | 10.1023/a:1000301702170 | 10.1007/bfb0085374 - f774854a-3939-4aa9-bf73-7e0573908b88 | e19ce792-422d-4feb-92ba-dd8536a60618 | 10.32835/2223-5752.2018.17.14-21 | 10.31652/2412-1142-2018-50-151-156 - 615ddf8c-2d91-4c1c-b04a-76b69f07b300 | e7af8377-9542-4711-9444-872f45521dc1 | 10.5644/sjm.10.1.00 | 10.5644/sjm.10.1.01 - 43fa1b53-eddb-4f31-96af-bc9bd3bb31b6 | e1ec5d8a-ff88-49f4-8540-73ee4906e119 | 10.1136/bjo.81.11.934 | 10.1038/sj.bjc.6690790 - 64b04cbc-ab3d-4cef-aff5-9d6b2532c47a | 43c387d1-e4c9-49f3-9995-552451a9a246 | 10.1023/a:1002015330987 | 10.1006/jnth.1998.2271 - 31e6e1a8-8457-4c93-82d3-12a51c0dc1bb | a2ec4305-63d2-4164-8470-02bf5c4ba74c | 10.1186/1742-4690-2-s1-s84 | 10.1038/nm0703-847 - 3461024a-1800-44a0-a7be-73f14bac99dd | 6849d39f-6bae-460b-8a9d-d6b86fbac2d3 | 10.17265/2328-2150/2014.11 | 10.1590/s0074-02762002000900009 - c2707e43-6a4b-4f5d-8fb4-babe16b42b4d | 82127faf-d125-4cd4-88b9-9a8618392019 | 10.1055/s-005-28993 | 10.1055/s-0034-1380711 - 0fe72304-1884-4dde-98c6-7cf3aec5bf31 | e3fe46cd-0205-42e4-8255-490e0eba38ea | 10.1787/5k4c1s0z2gs1-en | 10.1787/9789282105931-2-en - 686a1508-b6c5-4060-9035-1dd8a4b85be1 | dcecd03d-e0f6-40ce-a376-7e64bd90bdca | 10.15406/jlprr.2.3 | 10.15406/jlprr.2015.02.00039 - 9403bc0e-2a50-4c8a-ab79-943bce20e583 | 3073dee2-c8f7-42ed-a727-12306d86fa35 | 10.1787/5jrtgzfl6g9w-en | 10.1111/1468-2443.00004 - 9a080a6f-aaaf-4f4b-acab-3eda2bfacc22 | af28a167-2ddc-43db-98ca-1cc29b863f9f | 10.13040/ijpsr.0975-8232.4(6).2094-05 | 10.1002/chin.201418290 - 810f1a00-623f-4a5c-88e2-7240232ae8f9 | 639d4ddd-ef24-49dc-8d4e-ea626b0b85f8 | 10.13040/ijpsr.0975-8232.5(6).2216-24 | 10.1006/phrs.1997.0184 - 10.13040/IJPSR.0975-8232.5(6).2216-24 - 72752c59-9532-467d-8b4f-fe4d994bcff5 | cc3db36c-27e9-45bf-96b0-56d1119b93d6 | 10.22201/facmed.2007865xe.2018.26 | 10.22201/facmed.2007865x.2018.26.01 - a0740fc2-a1db-4bc8-ac98-177ccebde24f | 0a7136ac-86ad-4636-9c2a-b56a6d5a3a27 | 10.24966/cmph-1978/vol6iss1 | 10.1093/milmed/146.4.283 - 5b05df6a-7a0e-411b-a4e1-0081d7522673 | dc0cb585-c709-4990-a82e-c7c9b254fc74 | 10.15406/jig.3.1 | 10.15406/jig.2016.03.00039 - 011964dd-24a6-4d25-b9dd-921077f1947e | deabab6d-7381-4567-bf56-5294ab081e20 | 10.17265/1537-1506/2013.01 | 10.1109/icsssm.2016.7538527 - 4d7efa59-30c7-4015-bea9-d7df171a97ed | a05449a0-34d7-4f45-9b92-bcf71db4918d | 10.14413/herj.2017.01.09 | 10.14413/herj.2017.01.09. - (20 rows) - -Total counts, broken DOIs, by source: - - SELECT file_edit.extra_json->>'ingest_request_source' as source, COUNT(*) as broken_files - FROM file_edit - LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev - LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id - LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id - WHERE - file_edit.extra_json->>'link_source_id' IS NOT NULL - AND file_edit.extra_json->>'link_source_id' LIKE '10.%' - AND release_rev.doi != file_edit.extra_json->>'link_source_id' - GROUP BY file_edit.extra_json->>'ingest_request_source'; - - - source | broken_files - ------------------+-------------- - fatcat-changelog | 872 - unpaywall | 227954 - (2 rows) - -## Cleanup Pseudocode - -Dump file idents from above SQL queries. Transform from UUID to fatcat ident. - -For each file ident, fetch file entity, with releases expanded. Also fetch edit -history. Filter by: - -- single release for file -- single edit in history, matching broken agent -- edit metadata indicates a DOI, which doesn't match release DOI (or release doesn't have DOI?) - -If all that is the case, do a lookup by the correct DOI. If there is a match, -update the file entity to point to that release (and only that release). -Operate in batches. - -Write cleanup bot, run in QA to test. Run SQL query again and iterate if some -files were not updated. Merge to master, run full dump and update in prod. - -## Export Matches Needing Fix - - COPY ( - SELECT row_to_json(row.*) FROM ( - SELECT file_edit.ident_id as file_ident, release_ident.id as wrong_release_ident, file_edit.extra_json as edit_extra - FROM file_edit - LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev - LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id - LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id - WHERE - file_edit.extra_json->>'link_source_id' IS NOT NULL - AND file_edit.extra_json->>'link_source_id' LIKE '10.%' - AND release_rev.doi != file_edit.extra_json->>'link_source_id' - -- LIMIT 20; - ) as row - ) TO '/srv/fatcat/snapshots/file_release_bugfix_20211105.unfiltered.json'; - # COPY 228,827 - -Then need to do a `sed` pass, and a `rg` pass, to filter out bad escapes: - - cat /srv/fatcat/snapshots/file_release_bugfix_20211105.unfiltered.json \ - | sed 's/\\"/\"/g' \ - | rg -v "\\\\" \ - | rg '^\{' \ - | pv -l \ - > /srv/fatcat/snapshots/file_release_bugfix_20211105.json - # 228k 0:00:00 [ 667k/s] - - wc -l /srv/fatcat/snapshots/file_release_bugfix_20211105.json - # 228,826 - -And create a sample file: - - shuf -n10000 /srv/fatcat/snapshots/file_release_bugfix_20211105.json > /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json - - -## Testing in QA - - export FATCAT_AUTH_WORKER_CLEANUP=[...] - - head -n10 /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json \ - | python -m fatcat_tools.cleanups.file_release_bugfix - - # Counter({'total': 10, 'update': 10, 'skip': 0, 'insert': 0, 'exists': 0}) - - file_wmjzuybuorfrjdgnr2d32vg5va: was wrong, now correct, no other files - file_wgszcwehlffnzmoypr4l2yhvza: was correct, now correct, no other files. multiple articles in single PDF - file_p4r5sbminzgrhn4yaiqyr7ahwi: was correct, now wrong (!!!) - doi:10.1055/s-0036-1579844 - PDF says: 10.4103/0028-3886.158210 - unpaywall still has this incorrect linkage - file_n5jtvrnodbfdbccl5d6hshhvw4: now stub, was wrong - doi:10.19080/bboaj.2018.04.555640 release_suvtcm7hdbbr3fczcxxt4thgoi seems correct? - doi:10.19080/bboaj.4.4 is the bad DOI, not in fatcat. is registered, as an entire issue - file_kt5fv4d5lrbk7j3dxxgcm7hph4: was wrong, now correct - file_jq4juugnynhsdkh3whkcjod46q: was wrong, now correct - file_ef7w6y7k4jhjhgwmfai37yjjmm: was wrong, now correct - file_ca2svhd6knfnff4dktuonp45du: was correct, now correct. complicated, multiple DOIs/copies/files of same work - file_borst2aewvcwzhucnyth2vf3lm: was correct, now correct. complicated, multiple DOIs, single file of same work - -Overall, seems like this might not be as much of an obvious improvement as -hoped! But still progress and more correct. - - head -n1000 /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json \ - | python -m fatcat_tools.cleanups.file_release_bugfix - - # Counter({'total': 1000, 'update': 929, 'skip-existing-history-updated': 58, 'skip-existing-fixed': 10, 'skip': 3, 'skip-link-source': 3, 'insert': 0, 'exists': 0}) - -Looking at `skip-link-source`, it is cases where `link_source` is 'doi' not -'fatcat-changelog'. Will update filter behavior, 'fatcat-changelog' is a -`ingest_request_source`. - -Checking another 10 examples. They all seem to end up as correct matches. - -Did a small update and running the whole batch: - - cat /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json \ - | python -m fatcat_tools.cleanups.file_release_bugfix - - # Counter({'total': 10000, 'update': 8499, 'skip-existing-fixed': 939, 'skip-existing-history-updated': 560, 'skip': 2, 'skip-wrong-release-is-ok': 2, 'insert': 0, 'exists': 0}) - -I think this is ready to go! Example with parallel: - - cat /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json \ - | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.file_release_bugfix - - diff --git a/notes/cleanups/file_sha1_dedupe.md b/notes/cleanups/file_sha1_dedupe.md deleted file mode 100644 index 0829bc79..00000000 --- a/notes/cleanups/file_sha1_dedupe.md +++ /dev/null @@ -1,64 +0,0 @@ - - -## Prep - -Using `check_hashes.sh`: - - zcat $HASH_FILE \ - | awk '{print $3 "\t" $1}' \ - | rg -v '^\t' \ - | sort -S 4G \ - | uniq -D -w 40 \ - > sha1_ident.dupes.tsv - - wc -l sha1_ident.dupes.tsv - # 6,350 - - cut -f1 sha1_ident.dupes.tsv | uniq | wc -l - # 2,039 - -Want to create JSON for each group, like: - - entity_type: "file" - primary_id: str or None - duplicate_ids: [str] - evidence: - extid: str - extid_type: "sha1" - -Run transform script: - - cat sha1_ident.dupes.tsv | ./file_dupe_to_json.py | pv -l > file_sha1_dupes.json - # 2.04k 0:00:00 [9.16k/s] - - -## QA Testing - - export FATCAT_AUTH_API_TOKEN=[...] - - head -n25 /srv/fatcat/datasets/file_sha1_dupes.json \ - | python -m fatcat_tools.mergers.files --editgroup-description-override "Automated merging of file entities with duplicate SHA-1 hashes" --dry-run merge-files - - -Hit some small bugs running in QA; test coverage isn't great, but I think hits -the important parts. - - head -n25 /srv/fatcat/datasets/file_sha1_dupes.json \ - | python -m fatcat_tools.mergers.files --editgroup-description-override "Automated merging of file entities with duplicate SHA-1 hashes" --dry-run merge-files - - # Running in dry-run mode! - # Counter({'updated-entities': 60, 'lines': 25, 'merged': 25, 'skip': 0, 'updated-total': 0}) - -Dry-run mode didn't actually work, and edits actually happened (!). - -Edits do look good. - -Try again, not dry-run, to ensure that case is handled: - - head -n25 /srv/fatcat/datasets/file_sha1_dupes.json | python -m fatcat_tools.mergers.files --editgroup-description-override "Automated merging of file entities with duplicate SHA-1 hashes" merge-files - - # Counter({'lines': 25, 'skip': 25, 'skip-not-active-entity': 25, 'merged': 0, 'updated-total': 0}) - -And then run 500 through for more testing: - - head -n500 /srv/fatcat/datasets/file_sha1_dupes.json | python -m fatcat_tools.mergers.files --editgroup-description-override "Automated merging of file entities with duplicate SHA-1 hashes" merge-files - - # Counter({'updated-entities': 1341, 'lines': 500, 'merged': 474, 'skip': 26, 'skip-not-active-entity': 25, 'skip-entity-not-found': 1, 'updated-total': 0}) - -The majority of merges seem to be cases where there are multiple articles in the same PDF. diff --git a/notes/cleanups/scripts/container_dupe_to_json.py b/notes/cleanups/scripts/container_dupe_to_json.py deleted file mode 100755 index 2e841c69..00000000 --- a/notes/cleanups/scripts/container_dupe_to_json.py +++ /dev/null @@ -1,55 +0,0 @@ -#!/usr/bin/env python3 - -""" -This script can be used to transform duplicate container entity rows into JSON -objects which can be passed to the container entity merger. - -It is initially used to de-dupe ISSN-Ls. The script is based on -`file_dupe_to_json.py`. -""" - -import json, sys -from typing import Optional - -EXTID_TYPE = "issnl" - - -def print_group(extid, dupe_ids): - if len(dupe_ids) < 2: - return - group = dict( - entity_type="container", - primary_id=None, - duplicate_ids=dupe_ids, - evidence=dict( - extid=extid, - extid_type=EXTID_TYPE, - ), - ) - print(json.dumps(group, sort_keys=True)) - -def run(): - last_extid = None - dupe_ids = [] - for l in sys.stdin: - l = l.strip() - if not l: - continue - (row_extid, row_id) = l.split("\t")[0:2] - if EXTID_TYPE == "issnl": - assert len(row_extid) == 9 - else: - raise Exception(f"extid type not supported yet: {EXTID_TYPE}") - if row_extid == last_extid: - dupe_ids.append(row_id) - continue - elif dupe_ids: - print_group(last_extid, dupe_ids) - last_extid = row_extid - dupe_ids = [row_id] - if last_extid and dupe_ids: - print_group(last_extid, dupe_ids) - - -if __name__=="__main__": - run() diff --git a/notes/cleanups/scripts/fetch_full_cdx_ts.py b/notes/cleanups/scripts/fetch_full_cdx_ts.py deleted file mode 100644 index ebcf0d62..00000000 --- a/notes/cleanups/scripts/fetch_full_cdx_ts.py +++ /dev/null @@ -1,201 +0,0 @@ -#!/usr/bin/env python3 - -import sys -import json -import base64 -from typing import Optional, List - -import requests -from requests.adapters import HTTPAdapter -from requests.packages.urllib3.util.retry import Retry # pylint: disable=import-error - -def requests_retry_session( - retries: int = 10, - backoff_factor: int = 3, - status_forcelist: List[int] = [500, 502, 504], - session: requests.Session = None, -) -> requests.Session: - """ - From: https://www.peterbe.com/plog/best-practice-with-retries-with-requests - """ - session = session or requests.Session() - retry = Retry( - total=retries, - read=retries, - connect=retries, - backoff_factor=backoff_factor, - status_forcelist=status_forcelist, - ) - adapter = HTTPAdapter(max_retries=retry) - session.mount("http://", adapter) - session.mount("https://", adapter) - return session - -def b32_hex(s: str) -> str: - """ - Converts a base32-encoded SHA-1 checksum into hex-encoded - - base32 checksums are used by, eg, heritrix and in wayback CDX files - """ - s = s.strip().split()[0].lower() - if s.startswith("sha1:"): - s = s[5:] - if len(s) != 32: - if len(s) == 40: - return s - raise ValueError("not a base-32 encoded SHA-1 hash: {}".format(s)) - return base64.b16encode(base64.b32decode(s.upper())).lower().decode("utf-8") - - -SANDCRAWLER_POSTGREST_URL = "http://wbgrp-svc506.us.archive.org:3030" - -def get_db_cdx(url: str, http_session) -> List[dict]: - resp = http_session.get(SANDCRAWLER_POSTGREST_URL + "/cdx", params=dict(url="eq." + url)) - resp.raise_for_status() - rows = resp.json() - return rows or [] - -CDX_API_URL = "https://web.archive.org/cdx/search/cdx" - -def get_api_cdx(url: str, partial_dt: str, http_session) -> Optional[dict]: - - params = { - "url": url, - "from": partial_dt, - "to": partial_dt, - "matchType": "exact", - "output": "json", - "limit": 20, - # can't filter status because might be warc/revisit - #"filter": "statuscode:200", - } - resp = http_session.get(CDX_API_URL, params=params) - resp.raise_for_status() - rows = resp.json() - - if not rows: - return None - #print(rows, file=sys.stderr) - if len(rows) < 2: - return None - - for raw in rows[1:]: - record = dict( - surt=raw[0], - datetime=raw[1], - url=raw[2], - mimetype=raw[3], - status_code=raw[4], - sha1b32=raw[5], - sha1hex=b32_hex(raw[5]), - ) - if record['url'] != url: - # TODO: could allow HTTP/HTTPS fuzzy match - print("CDX API near match: URL", file=sys.stderr) - continue - if not record['datetime'].startswith(partial_dt): - print(f"CDX API near match: datetime {partial_dt} {record['datetime']}", file=sys.stderr) - continue - if record['status_code'] == "200" or (record['status_code'] == '-' and record['mimetype'] == 'warc/revisit'): - return record - else: - print(f"CDX API near match: status {record['status_code']}", file=sys.stderr) - return None - -def process_file(fe, session) -> dict: - short_urls = [] - self_urls = dict() - full_urls = dict() - status = "unknown" - - for pair in fe['urls']: - u = pair['url'] - if not '://web.archive.org/web/' in u: - continue - seg = u.split('/') - assert seg[2] == "web.archive.org" - assert seg[3] == "web" - if not seg[4].isdigit(): - continue - original_url = "/".join(seg[5:]) - if len(seg[4]) == 12 or len(seg[4]) == 4: - short_urls.append(u) - elif len(seg[4]) == 14: - self_urls[original_url] = u - else: - print(f"other bogus ts: {seg[4]}", file=sys.stderr) - return dict(file_entity=fe, full_urls=full_urls, status="fail-bogus-ts") - - if len(short_urls) == 0: - return dict(file_entity=fe, full_urls=[], status="skip-no-shorts") - - for short in list(set(short_urls)): - seg = short.split('/') - ts = seg[4] - assert len(ts) in [12,4] and ts.isdigit() - original_url = '/'.join(seg[5:]) - - if short in full_urls: - continue - - if original_url in self_urls and ts in self_urls[original_url]: - full_urls[short] = self_urls[original_url] - status = "success-self" - continue - - cdx_row_list = get_db_cdx(original_url, http_session=session) - for cdx_row in cdx_row_list: - if cdx_row['sha1hex'] == fe['sha1'] and cdx_row['url'] == original_url and cdx_row['datetime'].startswith(ts): - assert len(cdx_row['datetime']) == 14 and cdx_row['datetime'].isdigit() - full_urls[short] = f"https://web.archive.org/web/{cdx_row['datetime']}/{original_url}" - status = "success-db" - break - else: - #print(f"cdx DB found, but no match", file=sys.stderr) - pass - cdx_row = None - - if short in full_urls: - continue - - cdx_record = None - try: - cdx_record = get_api_cdx(original_url, partial_dt=ts, http_session=session) - except requests.exceptions.HTTPError as e: - if e.response.status_code == 403: - return dict(file_entity=fe, full_urls=full_urls, status="fail-cdx-403") - else: - raise - if cdx_record: - if cdx_record['sha1hex'] == fe['sha1'] and cdx_record['url'] == original_url and cdx_record['datetime'].startswith(ts): - assert len(cdx_record['datetime']) == 14 and cdx_record['datetime'].isdigit() - full_urls[short] = f"https://web.archive.org/web/{cdx_record['datetime']}/{original_url}" - status = "success-api" - break - else: - print(f"cdx API found, but no match", file=sys.stderr) - else: - print(f"no CDX API record found: {original_url}", file=sys.stderr) - - if short not in full_urls: - return dict(file_entity=fe, full_urls=full_urls, status="fail-not-found") - - return dict( - file_entity=fe, - full_urls=full_urls, - status=status, - ) - -def main(): - session = requests_retry_session() - session.headers.update({ - "User-Agent": "Mozilla/5.0 fatcat.CdxFixupBot", - }) - for line in sys.stdin: - if not line.strip(): - continue - fe = json.loads(line) - print(json.dumps(process_file(fe, session=session))) - -if __name__=="__main__": - main() diff --git a/notes/cleanups/scripts/file2ingestrequest.py b/notes/cleanups/scripts/file2ingestrequest.py deleted file mode 100755 index a005837f..00000000 --- a/notes/cleanups/scripts/file2ingestrequest.py +++ /dev/null @@ -1,44 +0,0 @@ -#!/usr/bin/env python3 - -from typing import Optional -import json, sys - - -def transform(row: dict) -> Optional[dict]: - if row.get('mimetype') not in [None, 'application/pdf']: - return None - if row.get('state') != 'active': - return None - base_url = None - for url in (row.get('urls') or []): - url = url['url'] - if '://web.archive.org/' not in url and '://archive.org/' not in url: - base_url = url - break - if not base_url: - return None - if not row.get('sha1'): - return None - return dict( - base_url=base_url, - ingest_type="pdf", - link_source="fatcat", - link_source_id=f"file_{row['ident']}", - ingest_request_source="file-backfill", - ext_ids=dict( - sha1=row['sha1'], - ), - ) - - -def run(): - for l in sys.stdin: - if not l.strip(): - continue - row = json.loads(l) - request = transform(row) - if request: - print(json.dumps(request, sort_keys=True)) - -if __name__=="__main__": - run() diff --git a/notes/cleanups/scripts/file_dupe_to_json.py b/notes/cleanups/scripts/file_dupe_to_json.py deleted file mode 100755 index 2064dc1c..00000000 --- a/notes/cleanups/scripts/file_dupe_to_json.py +++ /dev/null @@ -1,72 +0,0 @@ -#!/usr/bin/env python3 - -""" -This script can be used to transform duplicate file entity hash export rows -into JSON objects which can be passed to the file entity merger. - -The input is expected to be a TSV with two columns: a hash value in the first -column, and a fatcat file entity ident (in UUID format, not "fatcat ident" -encoded) in the second column. The rows are assumed to be sorted by hash value -(the first column), and duplicate values (same hash, differing UUID) are -contiguous. - -File hashes aren't really "external identifiers" (ext_id), but we treat them as -such here. - -Script is pretty simple, should be possible to copy and reuse for release, -container, creator entity duplicates. -""" - -import json, sys -from typing import Optional -import base64, uuid - -EXTID_TYPE = "sha1" - -def uuid2fcid(s: str) -> str: - """ - Converts a uuid.UUID object to a fatcat identifier (base32 encoded string) - """ - raw = uuid.UUID(s).bytes - return base64.b32encode(raw)[:26].lower().decode("utf-8") - -def print_group(extid, dupe_ids): - if len(dupe_ids) < 2: - return - group = dict( - entity_type="file", - primary_id=None, - duplicate_ids=dupe_ids, - evidence=dict( - extid=extid, - extid_type=EXTID_TYPE, - ), - ) - print(json.dumps(group, sort_keys=True)) - -def run(): - last_extid = None - dupe_ids = [] - for l in sys.stdin: - l = l.strip() - if not l: - continue - (row_extid, row_uuid) = l.split("\t")[0:2] - if EXTID_TYPE == "sha1": - assert len(row_extid) == 40 - else: - raise Exception(f"extid type not supported yet: {EXTID_TYPE}") - row_id = uuid2fcid(row_uuid) - if row_extid == last_extid: - dupe_ids.append(row_id) - continue - elif dupe_ids: - print_group(last_extid, dupe_ids) - last_extid = row_extid - dupe_ids = [row_id] - if last_extid and dupe_ids: - print_group(last_extid, dupe_ids) - - -if __name__=="__main__": - run() diff --git a/notes/cleanups/wayback_timestamps.md b/notes/cleanups/wayback_timestamps.md deleted file mode 100644 index 9db77058..00000000 --- a/notes/cleanups/wayback_timestamps.md +++ /dev/null @@ -1,304 +0,0 @@ - -At some point, using the arabesque importer (from targeted crawling), we -accidentally imported a bunch of files with wayback URLs that have 12-digit -timestamps, instead of the full canonical 14-digit timestamps. - - -## Prep (2021-11-04) - -Download most recent file export: - - wget https://archive.org/download/fatcat_bulk_exports_2021-10-07/file_export.json.gz - -Filter to files with problem of interest: - - zcat file_export.json.gz \ - | pv -l \ - | rg 'web.archive.org/web/\d{12}/' \ - | gzip \ - > files_20211007_shortts.json.gz - # 111M 0:12:35 - - zcat files_20211007_shortts.json.gz | wc -l - # 7,935,009 - - zcat files_20211007_shortts.json.gz | shuf -n10000 > files_20211007_shortts.10k_sample.json - -Wow, this is a lot more than I thought! - -There might also be some other short URL patterns, check for those: - - zcat file_export.json.gz \ - | pv -l \ - | rg 'web.archive.org/web/\d{1,11}/' \ - | gzip \ - > files_20211007_veryshortts.json.gz - # skipped, mergine with below - - zcat file_export.json.gz \ - | rg 'web.archive.org/web/None/' \ - | pv -l \ - > /dev/null - # 0.00 0:10:06 [0.00 /s] - # whew, that pattern has been fixed it seems - - zcat file_export.json.gz | rg '/None/' | pv -l > /dev/null - # 2.00 0:10:01 [3.33m/s] - - zcat file_export.json.gz \ - | rg 'web.archive.org/web/\d{13}/' \ - | pv -l \ - > /dev/null - # 0.00 0:10:09 [0.00 /s] - -Yes, 4-digit is a popular pattern as well, need to handle those: - - zcat file_export.json.gz \ - | pv -l \ - | rg 'web.archive.org/web/\d{4,12}/' \ - | gzip \ - > files_20211007_moreshortts.json.gz - # 111M 0:13:22 [ 139k/s] - - zcat files_20211007_moreshortts.json.gz | wc -l - # 9,958,854 - - zcat files_20211007_moreshortts.json.gz | shuf -n10000 > files_20211007_moreshortts.10k_sample.json - - -## Fetch Complete URL - -Want to export JSON like: - - file_entity - [existing file entity] - full_urls[]: list of Dicts[str,str] - <short_url>: <full_url> - status: str - -Status one of: - -- 'success-self': the file already has a fixed URL internally -- 'success-db': lookup URL against sandcrawler-db succeeded, and SHA1 matched -- 'success-cdx': CDX API lookup succeeded, and SHA1 matched -- 'fail-not-found': no matching CDX record found - -Ran over a sample: - - cat files_20211007_shortts.10k_sample.json | ./fetch_full_cdx_ts.py > sample_out.json - - cat sample_out.json | jq .status | sort | uniq -c - 5 "fail-not-found" - 576 "success-api" - 7212 "success-db" - 2207 "success-self" - - head -n1000 | ./fetch_full_cdx_ts.py > sample_out.json - - zcat files_20211007_veryshortts.json.gz | head -n1000 | ./fetch_full_cdx_ts.py | jq .status | sort | uniq -c - 2 "fail-not-found" - 168 "success-api" - 208 "success-db" - 622 "success-self" - -Investigating the "fail-not-found", they look like http/https URL -not-exact-matches. Going to put off handling these for now because it is a -small fraction and more delicate. - -Again with the broader set: - - cat files_20211007_moreshortts.10k_sample.json | ./fetch_full_cdx_ts.py > sample_out.json - - cat sample_out.json | jq .status | sort | uniq -c - 9 "fail-not-found" - 781 "success-api" - 6175 "success-db" - 3035 "success-self" - -While running a larger batch, got a CDX API error: - - requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://web.archive.org/cdx/search/cdx?url=https%3A%2F%2Fwww.psychologytoday.com%2Ffiles%2Fu47%2FHenry_et_al.pdf&from=2017&to=2017&matchType=exact&output=json&limit=20 - - org.archive.util.io.RuntimeIOException: org.archive.wayback.exception.AdministrativeAccessControlException: Blocked Site Error - -So maybe need to use credentials after all. - - -## Cleanup Process - -Other possible cleanups to run at the same time, which would not require -external requests or other context: - -- URL has ://archive.org/ link with rel=repository => rel=archive -- mimetype is bogus => clean mimetype -- bogus file => set some new extra field, like scope=stub or scope=partial (?) - -It looks like the rel swap is already implemented in `generic_file_cleanups()`. -From sampling it seems like the mimetype issue is pretty small, so not going to -bite that off now. The "bogus file" issue requires thought, so also skipping. - - -## Commands (old) - -Running with 8x parallelism to not break things; expecting some errors along -the way, may need to add handlers for connection errors etc: - - # OLD SNAPSHOT - zcat files_20211007_moreshortts.json.gz \ - | parallel -j8 --linebuffer --round-robin --pipe ./fetch_full_cdx_ts.py \ - | pv -l \ - | gzip \ - > files_20211007_moreshortts.fetched.json.gz - -At 300 records/sec, this should take around 9-10 hours to process. - - - -## Prep Again (2021-11-09) - -After fixing "sort" issue and re-dumping file entities (2021-11-05 snapshot). - -Filter again: - - # note: in the future use pigz instead of gzip here - zcat file_export.json.gz \ - | pv -l \ - | rg 'web.archive.org/web/\d{4,12}/' \ - | gzip \ - > files_20211105_moreshortts.json.gz - # 112M 0:13:27 [ 138k/s] - - zcat files_20211105_moreshortts.json.gz | wc -l - # 9,958,854 - # good, exact same number as previous snapshot - - zcat files_20211105_moreshortts.json.gz | shuf -n10000 > files_20211105_moreshortts.10k_sample.json - # done - - cat files_20211105_moreshortts.10k_sample.json \ - | ./fetch_full_cdx_ts.py \ - | pv -l \ - > files_20211105_moreshortts.10k_sample.fetched.json - # 10.0k 0:03:36 [46.3 /s] - - cat files_20211105_moreshortts.10k_sample.fetched.json | jq .status | sort | uniq -c - 13 "fail-not-found" - 774 "success-api" - 6193 "success-db" - 3020 "success-self" - -After tweaking `success-self` logic: - - 13 "fail-not-found" - 859 "success-api" - 6229 "success-db" - 2899 "success-self" - - -## Testing in QA - -Copied `sample_out.json` to fatcat QA instance and renamed as `files_20211007_moreshortts.10k_sample.fetched.json` - - # OLD ATTEMPT - export FATCAT_API_AUTH_TOKEN=[...] - head -n10 /srv/fatcat/datasets/files_20211007_moreshortts.10k_sample.fetched.json \ - | python -m fatcat_tools.cleanups.file_short_wayback_ts - - -Ran in to issues, iterated above. - -Trying again with updated script and sample file: - - export FATCAT_AUTH_WORKER_CLEANUP=[...] - - head -n10 /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \ - | python -m fatcat_tools.cleanups.file_short_wayback_ts - - # Counter({'total': 10, 'update': 10, 'skip': 0, 'insert': 0, 'exists': 0}) - -Manually inspected and these look good. Trying some repeats and larger batched: - - head -n10 /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \ - | python -m fatcat_tools.cleanups.file_short_wayback_ts - - # Counter({'total': 10, 'skip-revision-changed': 10, 'skip': 0, 'insert': 0, 'update': 0, 'exists': 0}) - - head -n1000 /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \ - | python -m fatcat_tools.cleanups.file_short_wayback_ts - - - [...] - bad replacement URL: partial_ts=201807271139 original=http://www.scielo.br/pdf/qn/v20n1/4918.pdf fix_url=https://web.archive.org/web/20170819080342/http://www.scielo.br/pdf/qn/v20n1/4918.pdf - bad replacement URL: partial_ts=201904270207 original=https://www.matec-conferences.org/articles/matecconf/pdf/2018/62/matecconf_iccoee2018_03008.pdf fix_url=https://web.archive.org/web/20190501060839/https://www.matec-conferences.org/articles/matecconf/pdf/2018/62/matecconf_iccoee2018_03008.pdf - bad replacement URL: partial_ts=201905011445 original=https://cdn.intechopen.com/pdfs/5886.pdf fix_url=https://web.archive.org/web/20190502203832/https://cdn.intechopen.com/pdfs/5886.pdf - [...] - - # Counter({'total': 1000, 'update': 969, 'skip': 19, 'skip-bad-replacement': 18, 'skip-revision-changed': 10, 'skip-bad-wayback-timestamp': 2, 'skip-status': 1, 'insert': 0, 'exists': 0}) - - -It looks like these "bad replacement URLs" are due to timestamp mismatches. Eg, the partial timestamp is not part of the final timestamp. - -Tweaked fetch script and re-ran: - - # Counter({'total': 1000, 'skip-revision-changed': 979, 'update': 18, 'skip-bad-wayback-timestamp': 2, 'skip': 1, 'skip-status': 1, 'insert': 0, 'exists': 0}) - -Cool. Sort of curious what the deal is with those `skip-bad-wayback-timestamp`. - -Run the rest through: - - cat /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \ - | python -m fatcat_tools.cleanups.file_short_wayback_ts - - # Counter({'total': 10000, 'update': 8976, 'skip-revision-changed': 997, 'skip-bad-wayback-timestamp': 14, 'skip': 13, 'skip-status': 13, 'insert': 0, 'exists': 0}) - -Should tweak batch size to 100 (vs. 50). - -How to parallelize import: - - # from within pipenv - cat /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \ - | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.file_short_wayback_ts - - - -## Full Batch Commands - -Running in bulk again: - - zcat files_20211105_moreshortts.json.gz \ - | parallel -j8 --linebuffer --round-robin --pipe ./fetch_full_cdx_ts.py \ - | pv -l \ - | gzip \ - > files_20211105_moreshortts.fetched.json.gz - -Ran in to one: `requests.exceptions.HTTPError: 503 Server Error: Service -Temporarily Unavailable for url: [...]`. Will try again, if there are more -failures may need to split up in smaller chunks. - -Unexpected: - - Traceback (most recent call last): - File "./fetch_full_cdx_ts.py", line 200, in <module> - main() - File "./fetch_full_cdx_ts.py", line 197, in main - print(json.dumps(process_file(fe, session=session))) - File "./fetch_full_cdx_ts.py", line 118, in process_file - assert seg[4].isdigit() - AssertionError - 3.96M 3:04:46 [ 357 /s] - -Ugh. - - zcat files_20211105_moreshortts.json.gz \ - | tac \ - | parallel -j8 --linebuffer --round-robin --pipe ./fetch_full_cdx_ts.py \ - | pv -l \ - | gzip \ - > files_20211105_moreshortts.fetched.json.gz - # 9.96M 6:38:43 [ 416 /s] - -Looks like the last small tweak was successful! This was with git commit -`cd09c6d6bd4deef0627de4f8a8a301725db01e14`. - - - zcat files_20211105_moreshortts.fetched.json.gz | jq .status | sort | uniq -c | sort -nr - 6228307 "success-db" - 2876033 "success-self" - 846844 "success-api" - 7583 "fail-not-found" - 87 "fail-cdx-403" - |