Merge branch 'bnewbold-cleanups-nov2021' into 'master'

Fatcat metadata cleanups/fixups, November 2021

Three cleanups implemented in this branch:

- update non-lowercase DOIs on releases (couple hundred thousand entities)
- fix incorrectly imported file/release pairs, on the file entity side (~250k entities)
- expand truncated wayback URL timestamps in file entities (up to 10 million entities)

Instead of proposals, there are documents for each cleanup in `notes/cleanups/`.

Have done spot testing of tens of thousands of entities each in QA, and confident about running in production.

Plan is to run updates in the order above. DOI and bugfix updates will go fairly fast; the wayback timestamp updates will go slower, and result in large re-indexing load both in fatcat and scholar, because both release and work entities will get triggered for update when file entities are updated.

1 files changed, 291 insertions, 0 deletions

diff --git a/notes/cleanups/wayback_timestamps.md b/notes/cleanups/wayback_timestamps.md
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+
+At some point, using the arabesque importer (from targetted crawling), we
+accidentially 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