move 'cleanups' directory from notes to extra/

11 files changed, 1306 insertions, 0 deletions

diff --git a/extra/cleanups/case_sensitive_dois.md b/extra/cleanups/case_sensitive_dois.md
new file mode 100644
index 00000000..1bf1901e
--- /dev/null
+++ b/extra/cleanups/case_sensitive_dois.md
@@ -0,0 +1,71 @@
+
+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/extra/cleanups/container_issnl_dedupe.md b/extra/cleanups/container_issnl_dedupe.md
new file mode 100644
index 00000000..a76bc961
--- /dev/null
+++ b/extra/cleanups/container_issnl_dedupe.md
@@ -0,0 +1,105 @@
+
+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/extra/cleanups/double_slash_dois.md b/extra/cleanups/double_slash_dois.md
new file mode 100644
index 00000000..d4e9ded6
--- /dev/null
+++ b/extra/cleanups/double_slash_dois.md
@@ -0,0 +1,46 @@
+
+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/extra/cleanups/file_meta.md b/extra/cleanups/file_meta.md
new file mode 100644
index 00000000..d99e821e
--- /dev/null
+++ b/extra/cleanups/file_meta.md
@@ -0,0 +1,152 @@
+
+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/extra/cleanups/file_release_ingest_bug.md b/extra/cleanups/file_release_ingest_bug.md
new file mode 100644
index 00000000..d818905b
--- /dev/null
+++ b/extra/cleanups/file_release_ingest_bug.md
@@ -0,0 +1,192 @@
+
+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/extra/cleanups/file_sha1_dedupe.md b/extra/cleanups/file_sha1_dedupe.md
new file mode 100644
index 00000000..0829bc79
--- /dev/null
+++ b/extra/cleanups/file_sha1_dedupe.md
@@ -0,0 +1,64 @@
+
+
+## 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/extra/cleanups/scripts/container_dupe_to_json.py b/extra/cleanups/scripts/container_dupe_to_json.py
new file mode 100755
index 00000000..2e841c69
--- /dev/null
+++ b/extra/cleanups/scripts/container_dupe_to_json.py
@@ -0,0 +1,55 @@
+#!/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/extra/cleanups/scripts/fetch_full_cdx_ts.py b/extra/cleanups/scripts/fetch_full_cdx_ts.py
new file mode 100644
index 00000000..ebcf0d62
--- /dev/null
+++ b/extra/cleanups/scripts/fetch_full_cdx_ts.py
@@ -0,0 +1,201 @@
+#!/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/extra/cleanups/scripts/file2ingestrequest.py b/extra/cleanups/scripts/file2ingestrequest.py
new file mode 100755
index 00000000..a005837f
--- /dev/null
+++ b/extra/cleanups/scripts/file2ingestrequest.py
@@ -0,0 +1,44 @@
+#!/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/extra/cleanups/scripts/file_dupe_to_json.py b/extra/cleanups/scripts/file_dupe_to_json.py
new file mode 100755
index 00000000..2064dc1c
--- /dev/null
+++ b/extra/cleanups/scripts/file_dupe_to_json.py
@@ -0,0 +1,72 @@
+#!/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/extra/cleanups/wayback_timestamps.md b/extra/cleanups/wayback_timestamps.md
new file mode 100644
index 00000000..9db77058
--- /dev/null
+++ b/extra/cleanups/wayback_timestamps.md
@@ -0,0 +1,304 @@
+
+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"
+