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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" + |