cleanups: truncated wayback PDFs from common crawl

2 files changed, 292 insertions, 0 deletions

diff --git a/extra/bulk_edits/2021-11-29_file_commoncrawl_truncated.md b/extra/bulk_edits/2021-11-29_file_commoncrawl_truncated.md
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+
+Some PDF files in wayback were crawled externally by the Common Crawl project,
+and are truncted to 128 KB (130775 bytes). This corrupts the PDF files, and
+they can not be read. We want to remove these from the catalog, or at least,
+mark them as non-archival and "truncated" (in `content_scope` field).
+
+See the cleanup file for prep, counts, and other background.
+
+There were over 600 file entities with the exact file size. Some are valid, but
+over 400 were found to be corrupt, and updated in the catalog. The majority
+seemed to have alternate captures and distinct file entities (not truncated).
+
+## Prod Commands
+
+Configure CLI:
+
+    export FATCAT_API_HOST=https://api.fatcat.wiki
+    export FATCAT_AUTH_WORKER_CLEANUP=[...]
+    export FATCAT_API_AUTH_TOKEN=$FATCAT_AUTH_WORKER_CLEANUP
+
+    fatcat-cli --version
+    fatcat-cli 0.1.6
+
+    fatcat-cli status
+         API Version: 0.5.0 (local)
+            API host: https://api.fatcat.wiki [successfully connected]
+      Last changelog: 5636508
+      API auth token: [configured]
+             Account: cleanup-bot [bot] [admin] [active]
+                      editor_vvnmtzskhngxnicockn4iavyxq
+
+Start small and review:
+
+    cat /srv/fatcat/datasets/truncated_sha1.txt \
+        | awk '{print "sha1:" $0}' \
+        | parallel -j1 fatcat-cli get {} --json \
+        | jq . -c \
+        | rg -v '"content_scope"' \
+        | rg 130775 \
+        | head -n10 \
+        | fatcat-cli batch update file release_ids= content_scope=truncated --description 'Flag truncated/corrupt PDFs (due to common crawl truncation)'
+    # editgroup_3mviue5zebge3d2lqafgkfgwqa
+
+Reviewed and all were corrupt. Running the rest of the batch:
+
+    cat /srv/fatcat/datasets/truncated_sha1.txt \
+        | awk '{print "sha1:" $0}' \
+        | parallel -j1 fatcat-cli get {} --json \
+        | jq . -c \
+        | rg -v '"content_scope"' \
+        | rg 130775 \
+        | fatcat-cli batch update file release_ids= content_scope=truncated --description 'Flag truncated/corrupt PDFs (due to common crawl truncation)' --auto-accept
+
+And then the other batch for review (no `--auto-accept`):
+
+    cat /srv/fatcat/datasets/unknown_sha1.txt \
+        | awk '{print "sha1:" $0}' \
+        | parallel -j1 fatcat-cli get {} --json \
+        | jq . -c \
+        | rg -v '"content_scope"' \
+        | rg 130775 \
+        | fatcat-cli batch update file release_ids= content_scope=truncated --description 'Flag truncated/corrupt PDFs (due to common crawl truncation)'
+    # editgroup_7l32piag7vho5d6gz6ee6zbtgi
+    # editgroup_cnoheod4jjbevdzez7m5z4o64i
+    # editgroup_w3fdmv4ffjeytnfjh32t5yovsq
+
+These files were *not* truncated:
+
+    file_2unklhykw5dwpotmslsldhlofy / 68821b6042a0a15fc788e99a400a1e7129d651a3
+    file_xyfssct5pvde3ebg64bxoudcri / 7f307ebc2ce71c5f8a32ea4a77319403c8b87d95
+    file_rrwbddwwrjg5tk4zyr5g63p2xi / ebe9f9d5d9def885e5a1ef220238f9ea9907dde1
+    file_5bbhyx6labaxniz3pm2lvkr3wq / e498ee945b57b2d556bb2ed4a7d83e103bb3cc07
+
+All the other "unknown" were, and were updated (editgroups accepted).
diff --git a/extra/cleanups/file_commoncrawl_truncated.md b/extra/cleanups/file_commoncrawl_truncated.md
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index 00000000..f74c5b22
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+
+There are a bunch of PDF captures in wayback, crawled by common crawl, which
+have been truncated at 128 KBytes (130775 bytes).
+
+Most of these were presumably imported before GROBID success was required for
+fatcat ingest.
+
+Fixup should wait until `fatcat_meta` cleanup has completed.
+
+## Fatcat Files
+
+Using an old snapshot, found 553 hits in elasticsearch. Index has not been
+updated in a long time. Filtering to only those with a wayback URL, found just
+415.
+
+Here are some broken examples:
+
+    https://fatcat.wiki/file/2e64rh3rc5gbvjzy2zux3qo36y
+    sha1:44b54e9d272620f4e0641cadc1aa496fced5a950
+    CDX warc_path:1224043144048_15-c/1224043303833_53.arc.gz
+    CDX dt:20081006225231
+
+    https://fatcat.wiki/file/n7ydoj6b6rhdhe4sc24lb7licq
+    sha1:5916db9e338f2d6845af47a3e19b82cc59079249
+    CDX warc_path:1216931712771_5-c/1216932408179_9.arc.gz
+    CDX dt:20080708202110
+
+    https://fatcat.wiki/file/iazux5lur5bfveraq6m7iewf5m
+    645ff8b602a0ea94fd28ce93bfea4ff2f65aa124
+    CDX warc_path:1216743864162_13-c/1216744138445_15.arc.gz
+    CDX dt:20080706111123
+
+This example seems fine (not broken):
+
+    https://fatcat.wiki/file/lww5omk3grejhb2mlml3tikywq
+
+Should be able to write a small function which can match on the Common Crawl
+`warc_path` format.
+
+
+## Sandcrawler SQL Exploration
+
+    SELECT COUNT(*)
+    FROM file_meta
+    WHERE
+        size_bytes = 130775;
+    # 4904
+
+## Proposed Cleanup
+
+There are not many of these in fatcat. Propose:
+
+0. wait until `file_meta` updates are complete, and re-dump metadata
+1. filter `file_meta` dump to entities having this file size (using `rg` and `jq` filter)
+2. for each, do a sandcrawler-db CDX read and check `warc_path` for common crawl pattern
+3. if it matches, update file with `file_scope=corrupt` or
+   `file_scope=truncated`, and remove `release_ids`, then print out file entity
+4. use fatcat-cli to update file entity
+
+## Future Mitigation
+
+Should have sandcrawler, and possibly fatcat ingest worker, check for
+size=130775 before accepting files. Probably in sandcrawler, so it can check
+for common crawl WARC item name.
+
+Could run a patch crawl to ensure we have some copy of all these URLs.
+
+## Commands
+
+    zcat ../2021-11-25/file_export.json.gz \
+        | pv -l \
+        | rg '"size":130775,' \
+        > possibly_truncated.json
+
+    wc -l possibly_truncated.json 
+    # 655
+
+Pretty few! At least one is not corrupt:
+
+    https://web.archive.org/web/20050909185221/http://www.nature.com:80/cgi-taf/DynaPage.taf?file=/bmt/journal/v31/n4/full/1703836a.html&filetype=pdf
+
+Fetching from sandcrawler-db:
+
+    http get http://wbgrp-svc506.us.archive.org:3030/pdf_meta sha1hex==eq.7d5093fa09dc174471e590aab252d875bdecc7ed
+
+    cat possibly_truncated.json \
+        | jq .sha1 -r \
+        | parallel -j8 curl 'http://wbgrp-svc506.us.archive.org:3030/file_meta?sha1hex=eq.{}' \
+        | jq . -c \
+        | pv -l \
+        > possibly_truncated.file_meta.json
+
+    rg '"sha1hex"' possibly_truncated.file_meta.json | wc -l
+    # 556
+
+    cat possibly_truncated.json \
+        | jq .sha1 -r \
+        | parallel -j8 curl 'http://wbgrp-svc506.us.archive.org:3030/pdf_meta?sha1hex=eq.{}' \
+        | jq . -c \
+        | pv -l \
+        > possibly_truncated.pdf_meta.json
+
+    cat possibly_truncated.pdf_meta.json | rg '"success"' | wc -l
+    # 66
+
+    rg '"status"' possibly_truncated.pdf_meta.json | wc -l
+    # 427
+
+    cat possibly_truncated.json \
+        | jq .sha1 -r \
+        | parallel -j8 curl 'http://wbgrp-svc506.us.archive.org:3030/grobid?sha1hex=eq.{}' \
+        | jq . -c \
+        | pv -l \
+        > possibly_truncated.grobid.json
+
+    cat possibly_truncated.grobid.json | rg '"success"' | wc -l
+    # 67
+
+    rg '"status"' possibly_truncated.grobid.json | wc -l
+    # 430
+
+    cat possibly_truncated.pdf_meta.json \
+        | rg '"parse-error"' \
+        | jq '.[0].sha1hex' -r \
+        | sort \
+        > truncated_sha1.txt
+
+    wc -l truncated_sha1.txt
+    # 360 truncated_sha1.txt
+
+    cat possibly_truncated.json \
+        | jq .sha1 -r \
+        | sort \
+        > possibly_sha1.txt
+
+    cat possibly_truncated.pdf_meta.json \
+        | rg '"success"' \
+        | jq '.[0].sha1hex' -r \
+        | sort \
+        > pdf_fine_sha1.txt
+
+    cat possibly_truncated.json \
+        | rg -v '"rel"' \
+        | jq .sha1 -r \
+        | sort \
+        > nourl_sha1.txt
+
+    comm -23 possibly_sha1.txt truncated_sha1.txt \
+        | comm -23 - pdf_fine_sha1.txt \
+        | comm -23 - nourl_sha1.txt \
+        > unknown_sha1.txt
+
+Randomly sampled 10 `truncated_sha1.txt` and all were broken PDFs.
+
+For the others, will need to re-run this after finishing `file_meta` work?
+
+## Prod Commands
+
+Configure CLI:
+
+    export FATCAT_API_HOST=https://api.fatcat.wiki
+    export FATCAT_AUTH_WORKER_CLEANUP=[...]
+    export FATCAT_API_AUTH_TOKEN=$FATCAT_AUTH_WORKER_CLEANUP
+
+    fatcat-cli --version
+    fatcat-cli 0.1.6
+
+    fatcat-cli status
+         API Version: 0.5.0 (local)
+            API host: https://api.fatcat.wiki [successfully connected]
+      Last changelog: 5636508
+      API auth token: [configured]
+             Account: cleanup-bot [bot] [admin] [active]
+                      editor_vvnmtzskhngxnicockn4iavyxq
+
+Start small and review:
+
+    cat /srv/fatcat/datasets/truncated_sha1.txt \
+        | awk '{print "sha1:" $0}' \
+        | parallel -j1 fatcat-cli get {} --json \
+        | jq . -c \
+        | rg -v '"content_scope"' \
+        | rg 130775 \
+        | head -n10 \
+        | fatcat-cli batch update file release_ids= content_scope=truncated --description 'Flag truncated/corrupt PDFs (due to common crawl truncation)'
+    # editgroup_3mviue5zebge3d2lqafgkfgwqa
+
+Reviewed and all were corrupt. Running the rest of the batch:
+
+    cat /srv/fatcat/datasets/truncated_sha1.txt \
+        | awk '{print "sha1:" $0}' \
+        | parallel -j1 fatcat-cli get {} --json \
+        | jq . -c \
+        | rg -v '"content_scope"' \
+        | rg 130775 \
+        | fatcat-cli batch update file release_ids= content_scope=truncated --description 'Flag truncated/corrupt PDFs (due to common crawl truncation)' --auto-accept
+
+And then the other batch for review (no `--auto-accept`):
+
+    cat /srv/fatcat/datasets/unknown_sha1.txt \
+        | awk '{print "sha1:" $0}' \
+        | parallel -j1 fatcat-cli get {} --json \
+        | jq . -c \
+        | rg -v '"content_scope"' \
+        | rg 130775 \
+        | fatcat-cli batch update file release_ids= content_scope=truncated --description 'Flag truncated/corrupt PDFs (due to common crawl truncation)'
+    # editgroup_7l32piag7vho5d6gz6ee6zbtgi
+    # editgroup_cnoheod4jjbevdzez7m5z4o64i
+    # editgroup_w3fdmv4ffjeytnfjh32t5yovsq
+
+These files were *not* truncated:
+
+    file_2unklhykw5dwpotmslsldhlofy / 68821b6042a0a15fc788e99a400a1e7129d651a3
+    file_xyfssct5pvde3ebg64bxoudcri / 7f307ebc2ce71c5f8a32ea4a77319403c8b87d95
+    file_rrwbddwwrjg5tk4zyr5g63p2xi / ebe9f9d5d9def885e5a1ef220238f9ea9907dde1
+    file_5bbhyx6labaxniz3pm2lvkr3wq / e498ee945b57b2d556bb2ed4a7d83e103bb3cc07
+
+All the other "unknown" were, and were updated (editgroups accepted).