aboutsummaryrefslogtreecommitdiffstats
path: root/notes
diff options
context:
space:
mode:
Diffstat (limited to 'notes')
-rw-r--r--notes/cleanups/case_sensitive_dois.md71
-rw-r--r--notes/cleanups/container_issnl_dedupe.md105
-rw-r--r--notes/cleanups/double_slash_dois.md46
-rw-r--r--notes/cleanups/file_meta.md152
-rw-r--r--notes/cleanups/file_release_ingest_bug.md192
-rw-r--r--notes/cleanups/file_sha1_dedupe.md64
-rwxr-xr-xnotes/cleanups/scripts/container_dupe_to_json.py55
-rw-r--r--notes/cleanups/scripts/fetch_full_cdx_ts.py201
-rwxr-xr-xnotes/cleanups/scripts/file2ingestrequest.py44
-rwxr-xr-xnotes/cleanups/scripts/file_dupe_to_json.py72
-rw-r--r--notes/cleanups/wayback_timestamps.md304
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"
-