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| author | Bryan Newbold <bnewbold@robocracy.org> | 2021-11-29 14:34:02 -0800 |
|---|---|---|
| committer | Bryan Newbold <bnewbold@robocracy.org> | 2021-11-29 14:34:02 -0800 |
| commit | c32154f2875a7fb9aac727013e1475cdd811e180 (patch) | |
| tree | f0e061498a101fa824995fb6ec9f91e7e44257e1 /extra/bulk_edits | |
| parent | c5ea2dba358624f4c14da0a1a988ae14d0edfd59 (diff) | |
| download | fatcat-c32154f2875a7fb9aac727013e1475cdd811e180.tar.gz fatcat-c32154f2875a7fb9aac727013e1475cdd811e180.zip | |
move notes/bulk_edits/ to extra/bulk_edits/
Diffstat (limited to 'extra/bulk_edits')
23 files changed, 1743 insertions, 0 deletions
diff --git a/extra/bulk_edits/2019-06-24_unpaywall_archiveorg.md b/extra/bulk_edits/2019-06-24_unpaywall_archiveorg.md new file mode 100644 index 00000000..2f3bbb98 --- /dev/null +++ b/extra/bulk_edits/2019-06-24_unpaywall_archiveorg.md @@ -0,0 +1,262 @@ + +Goal is to import: + +- UNPAYWALL-PDF-CRAWL-2019-04.published dataset; about 6 million lines, expect + about half (3 million) new release fulltext matches +- archive.org fulltext, about 1.8 million files + +## QA UNPAYWALL-PDF-CRAWL-2019-04 + + export FATCAT_AUTH_WORKER_CRAWL=... + + # this wasn't a random sample + zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | head -n200 | ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04 + + # this was! + zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | shuf -n200 | ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04 + [...] + Counter({'total': 199, 'insert': 106, 'exists': 62, 'skip': 31, 'skip-extid-not-found': 20, 'skip-update-disabled': 1, 'update': 0}) + + # ok, big import + zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04 + # ran a few hundred thousand and looked good + +## prod UNPAYWALL-PDF-CRAWL-2019-04 + + export FATCAT_AUTH_WORKER_CRAWL=... + + zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | shuf -n200 | ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04 + Counter({'total': 198, 'insert': 115, 'exists': 56, 'skip': 27, 'skip-extid-not-found': 13, 'skip-update-disabled': 2, 'update': 0}) + + zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04 + [...] + Requiring GROBID status == 200 + Counter({'total': 520139, 'insert': 282524, 'exists': 155371, 'skip': 82244, 'skip-extid-not-found': 40000, 'skip-update-disabled': 6319, 'update': 0}) + 19008.63user 729.06system 3:01:57elapsed 180%CPU (0avgtext+0avgdata 51440maxresident)k + 8552inputs+4335032outputs (54major+370893minor)pagefaults 0swaps + + (loosely repeated 12x times, of course) + + oh no, lots of duplicate inserts... ugh. needed a uniq in there, but really + only "one hit per file" export. or a shuf? blech. + + (python)fatcat@wbgrp-svc502:/srv/fatcat/datasets$ zcat UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | jq .final_sha1 -r | sort -S 4G -u | wc -l + 5621882 + (python)fatcat@wbgrp-svc502:/srv/fatcat/datasets$ zcat UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | wc -l + 6181191 + + ugh. how did this get missed in QA? sloppy. + +fixup is going to be +- filter input list for duplicated sha1hex +- for each duplicated sha1hex: + - fetch file entity. if not single release_id, bail + - fetch release expanded with files + - find all files with same sha1 that *aren't* the fetched file + - print file entity id +- iterate over file entity ids, batches of 100x + - create editgroup + - delete files + - accept editgroup + +fetch_dupes.py: + + + #!/usr/bin/env python3 + + import sys + import fatcat_client + from fatcat_tools import public_api + + def do_sha1(api, sha1hex): + try: + fe = api.lookup_file(sha1=sha1hex) + except: + return + if len(fe.release_ids) != 1: + return + try: + re = api.get_release(fe.release_ids[0], expand='files', hide='refs,contribs,abstracts') + except: + return + for f in re.files: + if f.sha1 == fe.sha1 and f.ident != fe.ident and f.release_ids == [re.ident]: + print(f.ident) + + def run(): + api = public_api('https://api.qa.fatcat.wiki/v0') + for l in sys.stdin: + if l: + do_sha1(api, l.strip()) + + if __name__ == '__main__': + run() + +delete_dupes.py: + + + #!/usr/bin/env python3 + + import sys + import fatcat_client + from fatcat_tools import authenticated_api + + #API_ENDPOINT = 'https://api.qa.fatcat.wiki/v0' + API_ENDPOINT = 'https://api.fatcat.wiki/v0' + + def do_batch(api, batch): + eg = api.create_editgroup( + fatcat_client.Editgroup(description="Cleaning up duplicated file insertions from UNPAYWALL-CRAWL-2019-04 insert")) + for ident in batch: + api.delete_file(eg.editgroup_id, ident) + api.accept_editgroup(eg.editgroup_id) + print("deleted {} - {}...".format(eg.editgroup_id, len(batch))) + + def run(): + api = authenticated_api(API_ENDPOINT) + batch = [] + for l in sys.stdin: + l = l.strip() + if not l: + continue + try: + fe = api.get_file(l) + except: + continue + if fe.state == 'active' and fe.release_ids: + batch.append(l) + if len(batch) >= 100: + do_batch(api, batch) + batch = [] + if batch: + do_batch(api, batch) + + if __name__ == '__main__': + run() + +commands: + + zcat UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | jq .final_sha1 -r | b32_hex.py | sort -S 4G | uniq -d > repeated_sha1.tsv + + cat repeated_sha1.tsv | pv -l | ./fetch_dupes.py > repeated_file_idents.tsv + + export FATCAT_API_AUTH_TOKEN=... (crawl bot) + cat repeated_file_idents.tsv | ./delete_dupes.py + +## QA archive.org files + +Start with arxiv: + + # FATCAT_AUTH_WORKER_ARCHIVE_ORG + export FATCAT_API_AUTH_TOKEN=... + + # had a 500 "unexpected internal error: invalid length at 196", which was + due to syntax error in API token. should have a better error response + + # try sample of arxiv_id + zcat /srv/fatcat/datasets/arxiv.match.json.gz | head -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + Counter({'skip': 100, 'total': 100, 'skip-no-releases': 72, 'skip-no-urls': 28, 'update': 0, 'insert': 0, 'exists': 0}) + + # TODO: shouldn't re-insert if URL already in there under a different reltyp + + # Ok, made a bunch of code changes to "clean up" at least arxiv URLs. All + # arxiv.org files should be 1-to-1 with releases that have full arxiv_ids + +Ok, try JSTOR: + + zcat /srv/fatcat/datasets/jstor.match.json.gz | shuf -n1000 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + [...] + Counter({'total': 1000, 'skip': 763, 'skip-no-releases': 763, 'insert': 162, 'exists': 74, 'update': 1}) + +larger import got: + + HTTP response body: {"success":false,"error":"ConstraintViolation","message":"unexpected database error: duplicate key value violates unique constraint \"file_edit_editgroup_id_ident_id_key\""} + +could try getting around this with shuf? + + zcat /srv/fatcat/datasets/jstor.match.json.gz | shuf | pv -l | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + +got the same errors so added "inflight" edit protection and rolled back to earlier command: + + zcat /srv/fatcat/datasets/jstor.match.json.gz | shuf -n1000 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + [...] + 451k 0:25:32 [ 294 /s] + Counter({'total': 451178, 'skip-no-releases': 351287, 'skip': 351287, 'insert': 59644, 'exists': 39198, 'update': 1049, 'skip-update-inflight': 26}) + +many/most of these files were already in fatcat due to earlier "paper-manifest" +work... keep forgetting that! + +ok, next pmc: + + zcat /srv/fatcat/datasets/pmc.match.json.gz | shuf -n1000 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + [...] + Counter({'total': 1000, 'exists': 895, 'insert': 77, 'skip-no-releases': 22, 'skip': 22, 'update': 6}) + + that's a surprisingly large fraction (2.2%) with `skip-no-releases`. some + because pubmed import failed, some because multiple PMCID identifiers? hrm. + +ok, an finally paper-doi: + + zcat /srv/fatcat/datasets/paper-doi.match.json.gz | shuf -n1000 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + [...] + Counter({'total': 1000, 'exists': 720, 'insert': 280, 'update': 0, 'skip': 0}) + + lots exist! probably from the pre-1923 stuff? yup. + +## prod archive.org files + + # try sample of arxiv_id + zcat /srv/fatcat/datasets/arxiv.match.json.gz | shuf -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + Counter({'total': 100, 'insert': 80, 'update': 20, 'exists': 0, 'skip': 0}) + + # all arxiv_id + zcat /srv/fatcat/datasets/arxiv.match.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --editgroup-description-override '"Import fulltext from archive.org journals collection"' matched --default-mimetype application/pdf --default-link-rel archive - + [...] + Counter({'total': 62296, 'insert': 49503, 'update': 12413, 'exists': 269, 'skip': 111, 'skip-no-releases': 111, 'skip-update-inflight': 10}) + 2497.78user 98.87system 27:31.22elapsed 157%CPU (0avgtext+0avgdata 47604maxresident)k + 360inputs+266104outputs (3major+265297minor)pagefaults 0swaps + + # derp, some of those were crawl-bot but should have been archive-org-bot. ctrl-c and re-ran + + # sample jstor + zcat /srv/fatcat/datasets/jstor.match.json.gz | shuf -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + Counter({'total': 100, 'insert': 69, 'exists': 29, 'update': 1, 'skip': 1, 'skip-no-releases': 1}) + + # all jstor + zcat /srv/fatcat/datasets/jstor.match.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --editgroup-description-override '"Import fulltext from archive.org journals collection"' matched --default-mimetype application/pdf --default-link-rel archive - + [...] + Counter({'total': 41072, 'insert': 27783, 'exists': 11926, 'update': 1307, 'skip-update-inflight': 117, 'skip': 56, 'skip-no-releases': 56}) + 1257.93user 54.42system 12:45.96elapsed 171%CPU (0avgtext+0avgdata 45248maxresident)k + 5384inputs+157016outputs (38major+259749minor)pagefaults 0swaps + + good, pretty low `skip-no-releases` for JSTOR imports + + # sample pmc + zcat /srv/fatcat/datasets/pmc.match.json.gz | shuf -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + Counter({'total': 100, 'exists': 92, 'insert': 5, 'skip-no-releases': 2, 'skip': 2, 'update': 1}) + + interesting, at least one longtail file which is actually known: https://fatcat.wiki/file/xnc3sarc3jfsnceeagn34zi5la + almost all known! + + # all pmc + zcat /srv/fatcat/datasets/pmc.match.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --editgroup-description-override '"Import fulltext from archive.org journals collection"' matched --default-mimetype application/pdf --default-link-rel archive - + [...] + Counter({'total': 18720, 'exists': 16701, 'insert': 1461, 'skip': 357, 'skip-no-releases': 357, 'update': 201, 'skip-update-inflight': 1}) + + # sample paper-doi + zcat /srv/fatcat/datasets/paper-doi.match.json.gz | shuf -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive - + Counter({'total': 100, 'exists': 73, 'insert': 27, 'skip': 0, 'update': 0}) + + # all paper-doi + zcat /srv/fatcat/datasets/paper-doi.match.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --editgroup-description-override '"Import fulltext from archive.org journals collection"' matched --default-mimetype application/pdf --default-link-rel archive - + Counter({'total': 3014, 'exists': 2280, 'insert': 734, 'update': 0, 'skip': 0}) + Counter({'total': 3464, 'exists': 2483, 'insert': 981, 'update': 0, 'skip': 0}) + Counter({'total': 3437, 'exists': 2303, 'insert': 1134, 'update': 0, 'skip': 0}) + Counter({'total': 3450, 'exists': 2379, 'insert': 1071, 'update': 0, 'skip': 0}) + Counter({'total': 3467, 'exists': 2486, 'insert': 981, 'skip': 0, 'update': 0}) + Counter({'total': 3481, 'exists': 2583, 'insert': 898, 'skip': 0, 'update': 0}) + Counter({'total': 3423, 'exists': 2178, 'insert': 1245, 'update': 0, 'skip': 0}) + 62.41user 3.17system 0:31.18elapsed 210%CPU (0avgtext+0avgdata 49852maxresident)k + 96inputs+13184outputs (7major+159215minor)pagefaults 0swaps + +All done! diff --git a/extra/bulk_edits/2019-09-03_chocula.md b/extra/bulk_edits/2019-09-03_chocula.md new file mode 100644 index 00000000..03311c8c --- /dev/null +++ b/extra/bulk_edits/2019-09-03_chocula.md @@ -0,0 +1,23 @@ + +Ran on my laptop, from master branch (`00e4ec6865782e4453d4dcec24ee205bf7c13ecf`). + +In QA: + + time ./fatcat_import.py --host-url https://api.qa.fatcat.wiki/v0 chocula ~/code/chocula/export_fatcat.json + [...] + Counter({'total': 139032, 'exists': 76952, 'exists-skip-update': 65528, 'update': 46157, 'insert': 13605, 'exists-by-issnl': 8879, 'exists-not-found': 2538, 'skip': 2318, 'skip-unknown-new-issnl': 2318, 'exists-inactive': 7}) + real 32m30.009s + user 4m44.176s + sys 0m12.544s + +In prod: + + time ./fatcat_import.py --host-url https://api.fatcat.wiki/v0 chocula ~/code/chocula/export_fatcat.2019-09-03.json + + Counter({'total': 139032, 'update': 66802, 'exists': 47586, 'exists-skip-update': 47428, 'insert': 22326, 'skip-unknown-new-issnl': 2318, 'skip': 2318, 'exists-by-issnl': 158}) + + real 34m16.930s + user 5m5.116s + sys 0m13.560s + +The container auto-updater is currently broken, so needed to manually dump/load into elastic. diff --git a/extra/bulk_edits/2019-10-08_file_cleanups.md b/extra/bulk_edits/2019-10-08_file_cleanups.md new file mode 100644 index 00000000..2eebb363 --- /dev/null +++ b/extra/bulk_edits/2019-10-08_file_cleanups.md @@ -0,0 +1,59 @@ + +These cleanups are primarily intended to fix bogus 'None' datetime links to +wayback for files that are actually in petabox (archive.org not +web.archive.org). These URLs were created accidentally during fatcat +boostrapping; there are about 300k such file enties to fix. + +Will also update archive.org link reltype to 'archive' (instead of +'repository'), which is the new preferred style. + +Generated the set of files to update like: + + zcat file_export.2019-07-07.json.gz | rg 'web.archive.org/web/None' | gzip > file_export.2019-07-07.None.json.gz + + zcat /srv/fatcat/datasets/file_export.2019-07-07.None.json.gz | wc -l + 304308 + +## QA + +Running at git rev: + + 984a1b157990f42f8c57815f4b3c00f6455a114f + +Created a new 'cleanup-bot' account and credentials. Put token in local env. + +Ran with a couple hundred entities first; edits look good. + + zcat /srv/fatcat/datasets/file_export.2019-07-07.None.json.gz | head -n200 | ./fatcat_cleanup.py files - + +Then the full command, with batchsize=100: + + time zcat /srv/fatcat/datasets/file_export.2019-07-07.None.json.gz | pv -l | ./fatcat_cleanup.py --batch-size 100 files - + +Should finish in a couple hours. + + 304k 1:05:19 [77.6 /s] + + Counter({'cleaned': 304308, 'lines': 304308, 'updated': 297308, 'skip-revision': 7000}) + + real 65m20.613s + user 20m40.828s + sys 0m34.492s + +## Production + +Again ran with a couple hundred entities first; edits look good. + + zcat /srv/fatcat/datasets/file_export.2019-07-07.None.json.gz | head -n200 | ./fatcat_cleanup.py files - + +Then the full command, with batchsize=100: + + time zcat /srv/fatcat/datasets/file_export.2019-07-07.None.json.gz | pv -l | ./fatcat_cleanup.py --batch-size 100 files - + [...] + 304k 1:03:10 [80.3 /s] + Counter({'cleaned': 304308, 'lines': 304308, 'updated': 304107, 'skip-revision': 201}) + + real 63m11.631s + user 21m8.504s + sys 0m31.888s + diff --git a/extra/bulk_edits/2019-11-05_crossref_patch.md b/extra/bulk_edits/2019-11-05_crossref_patch.md new file mode 100644 index 00000000..1765fc36 --- /dev/null +++ b/extra/bulk_edits/2019-11-05_crossref_patch.md @@ -0,0 +1,58 @@ + +Goal is to make sure we have imported all in-scope crossref DOI objects. There +were a few months gap between the snapshot used as initial bootstrap and the +start of continuous ingest; any DOIs registered during that gap and not updated +since are not in fatcat. Expectation is that this will be a relatively small +import. + +## QA Run + +Started Thu 31 Oct 2019 08:07:20 PM PDT + + export FATCAT_AUTH_WORKER_CROSSREF="..." + time xzcat /srv/fatcat/datasets/crossref-works.2019-09-09.json.xz | time parallel -j20 --round-robin --pipe ./fatcat_import.py crossref - /srv/fatcat/datasets/20181203.ISSN-to-ISSN-L.txt --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3 + + # postgresql DB at start: fresh 2019-10 dump imported, 357 GB + # over 15k TPS against postgres + + 20x theads of: + Counter({'total': 5397349, 'exists': 4961058, 'skip': 360156, 'insert': 76135, 'inserted.container': 113, 'update': 0}) + + real 1173m52.497s => 20hr + user 13058m24.460s + sys 319m27.716s + + 1.5 million new releases + 7.2 million skips (total) + +Ran again with null subtitle fix and granular stats: + + 20x threads of: + Counter({'total': 5368366, 'exists': 5122104, 'skip': 244072, 'skip-blank-title': 38399, 'skip-release-type': 5296, 'insert': 2190, 'skip-huge-contribs': 70, 'skip-huge-refs': 7, 'update': 0}) + + 43k additional insets (still about 1.5m total) + of 4.8 million skipped (why not closer to 7.2 million?), most seem to be blank title + +## Production Run + +Git: 44c23290c72ec67db38f1e1d40b76ba795b40d9d + +started around Tue 05 Nov 2019 02:51:19 PM PST + + export FATCAT_AUTH_WORKER_CROSSREF="..." + time xzcat /srv/fatcat/datasets/crossref-works.2019-09-09.json.xz | time parallel -j20 --round-robin --pipe ./fatcat_import.py crossref - /srv/fatcat/datasets/20190730.ISSN-to-ISSN-L.txt --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3 + + # postgresql DB at start: 399.03G + + # 20x of: + Counter({'total': 5347938, 'exists': 5023305, 'skip': 251747, 'skip-blank-title': 247969, 'insert': 72886, 'skip-release-type': 3686, 'inserted.container': 103, 'skip-huge-contribs': 88, 'skip-huge-refs': 4, 'update': 0}) + # 1.45m new releases + # 2k more new containers + # 4.96m blank titles + + real 1139m42.231s + user 13307m10.124s + sys 355m18.904s + + # postgresql DB: 402.76G + diff --git a/extra/bulk_edits/2019-12-20_orcid.md b/extra/bulk_edits/2019-12-20_orcid.md new file mode 100644 index 00000000..33dde32f --- /dev/null +++ b/extra/bulk_edits/2019-12-20_orcid.md @@ -0,0 +1,43 @@ + +Newer ORCID dumps are XML, not JSON. But there is a conversion tool! + + https://github.com/ORCID/orcid-conversion-lib + +Commands: + + wget https://github.com/ORCID/orcid-conversion-lib/raw/master/target/orcid-conversion-lib-0.0.2-full.jar + java -jar orcid-conversion-lib-0.0.2-full.jar OPTIONS + + java -jar orcid-conversion-lib-0.0.2-full.jar --tarball -i ORCID_2019_summaries.tar.gz -v v3_0rc1 -o ORCID_2019_summaries_json.tar.gz + + # [...] + # Sat Dec 21 04:43:50 UTC 2019 done 7300000 + # Sat Dec 21 04:44:08 UTC 2019 done 7310000 + # Sat Dec 21 04:44:17 UTC 2019 finished errors 0 + +Importing in QA, ran in to some lines like: + + {"response-code":409,"developer-message":"409 Conflict: The ORCID record is locked and cannot be edited. ORCID https://orcid.org/0000-0003-0014-6598","user-message":"The ORCID record is locked.","error-code":9018,"more-info":"https://members.orcid.org/api/resources/troubleshooting"} + {"response-code":409,"developer-message":"409 Conflict: The ORCID record is locked and cannot be edited. ORCID https://orcid.org/0000-0003-3750-5654","user-message":"The ORCID record is locked.","error-code":9018,"more-info":"https://members.orcid.org/api/resources/troubleshooting"} + {"response-code":409,"developer-message":"409 Conflict: The ORCID record is locked and cannot be edited. ORCID https://orcid.org/0000-0003-1424-4826","user-message":"The ORCID record is locked.","error-code":9018,"more-info":"https://members.orcid.org/api/resources/troubleshooting"} + {"response-code":409,"developer-message":"409 Conflict: The ORCID record is locked and cannot be edited. ORCID https://orcid.org/0000-0002-5340-9665","user-message":"The ORCID record is locked.","error-code":9018,"more-info":"https://members.orcid.org/api/resources/troubleshooting"} + +Needed to patch to filter those out. Then ran ok like: + + zcat /srv/fatcat/datasets/ORCID_2019_summaries.sample_10k.json.gz | ./fatcat_import.py orcid - + Counter({'total': 10000, 'exists': 5323, 'insert': 4493, 'skip': 184, 'skip-no-person': 160, 'update': 0}) + +New dump is about 7.3 million rows, so expecting about 3.2 million new +entities, 250k skips. + +Doing bulk run like: + + time zcat /srv/fatcat/datasets/ORCID_2019_summaries.json.gz | parallel -j8 --round-robin --pipe ./fatcat_import.py orcid - + +Prod timing: + + Counter({'total': 910643, 'exists': 476812, 'insert': 416583, 'skip': 17248, 'update': 0}) + + real 47m27.658s + user 245m44.272s + sys 14m50.836s diff --git a/extra/bulk_edits/2019-12-20_updates.md b/extra/bulk_edits/2019-12-20_updates.md new file mode 100644 index 00000000..bd069a7a --- /dev/null +++ b/extra/bulk_edits/2019-12-20_updates.md @@ -0,0 +1,137 @@ + +## Arxiv + +Used metha-sync tool to update. Then went in raw storage directory (as opposed +to using `metha-cat`) and plucked out weekly files updated since last import. +Created a tarball and uploaded to: + + https://archive.org/download/arxiv_raw_oai_snapshot_2019-05-22/arxiv_20190522_20191220.tar.gz + +Downloaded, extracted, then unzipped: + + gunzip *.gz + +Run importer: + + export FATCAT_AUTH_WORKER_ARXIV=... + + ./fatcat_import.py --batch-size 100 arxiv /srv/fatcat/datasets/arxiv_20190522_20191220/2019-05-31-00000000.xml + # Counter({'exists': 1785, 'total': 1001, 'insert': 549, 'skip': 1, 'update': 0}) + + fd .xml /srv/fatcat/datasets/arxiv_20190522_20191220/ | parallel -j15 ./fatcat_import.py --batch-size 100 arxiv {} + +Things seem to run smoothly in QA. New releases get grouped with old works +correctly, no duplication obvious. + +In prod, loaded just the first file as a start, waiting to see if auto-ingest +happens. Looks like yes! Great that everything is so smooth. All seem to be new +captures. + +In production prod elasticsearch, 2,377,645 arxiv releases before this +updated import, 741,033 with files attached. Guessing about 150k new releases, +but will check. + +Up to 2,531,542 arxiv releases, so only 154k or so new releases created. +781,122 with fulltext. + +## Pubmed QA + +Grabbed fresh 2020 baseline, released in December 2019: <https://archive.org/details/pubmed_medline_baseline_2020> + + gunzip *.xml.gz + +Run importer: + + export FATCAT_AUTH_WORKER_PUBMED=... + + ./fatcat_import.py pubmed /srv/fatcat/datasets/pubmed_medline_baseline_2020/pubmed20n1000.xml /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + + # Counter({'total': 29975, 'update': 26650, 'skip': 2081, 'insert': 1193, 'warn-pmid-doi-mismatch': 36, 'exists': 36, 'skip-update-conflict': 15, 'inserted.container': 3}) + +Noticed that `release_year` was not getting set for many releases. Made a small +code tweak (`1bb0a2181d5a30241d80279c5930eb753733f30b`) and trying another: + + time ./fatcat_import.py pubmed /srv/fatcat/datasets/pubmed_medline_baseline_2020/pubmed20n1001.xml /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + + # Counter({'total': 30000, 'update': 25912, 'skip': 2119, 'insert': 1935, 'exists': 29, 'warn-pmid-doi-mismatch': 27, 'skip-update-conflict': 5, 'inserted.container': 1}) + + real 30m45.044s + user 16m43.672s + sys 0m10.792s + + time fd '.xml$' /srv/fatcat/datasets/pubmed_medline_baseline_2020 | time parallel -j16 ./fatcat_import.py pubmed {} /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + +More errors: + + HTTP response body: {"success":false,"error":"MalformedExternalId","message":"external identifier doesn't match required pattern for a DOI (expected, eg, '10.1234/aksjdfh'): 10.3760/cma. j. issn.2095-4352. 2014. 07.014"} + HTTP response body: {"success":false,"error":"MalformedExternalId","message":"external identifier doesn't match required pattern for a DOI (expected, eg, '10.1234/aksjdfh'): 10.13201/j.issn.10011781.2016.06.002"} + HTTP response body: {"success":false,"error":"MalformedExternalId","message":"external identifier doesn't match required pattern for a DOI (expected, eg, '10.1234/aksjdfh'): 10.23750/abm.v88i2 -s.6506"} + + + 10.1037//0002-9432.72.1.50 + BOGUS DOI: 10.1037//0021-843x.106.2.266 + BOGUS DOI: 10.1037//0021-843x.106.2.280 + => actual ok? at least redirect ok + + unparsable medline date, skipping: Summer 2018 + +TODO: +x fix bad DOI error (real error, skip these) +x remove newline after "unparsable medline date" error +x remove extra line like "existing.ident, existing.ext_ids.pmid, re.ext_ids.pmid))" in warning + +NOTE: Remember having run through the entire baseline in QA, but didn't save the command or output. + +## Pubmed Prod (2020-01-17) + +This is after adding a flag to enforce no updates at all, only new releases. +Will likely revisit and run through with updates that add important metadata +like exact references matches for older releases, after doing release +merge/group cleanups. + + + # git commit: d55d45ad667ccf34332b2ce55e8befbd212922ec + # had a trivial typo in fatcat_import.py, will push a fix + export FATCAT_AUTH_WORKER_PUBMED=... + time ./fatcat_import.py pubmed /srv/fatcat/datasets/pubmed_medline_baseline_2020/pubmed20n1001.xml /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + +Full run: + + fd '.xml$' /srv/fatcat/datasets/pubmed_medline_baseline_2020 | time parallel -j16 ./fatcat_import.py pubmed {} /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + + [...] + Command exited with non-zero status 2 + 1271708.20user 23689.44system 31:42:15elapsed 1134%CPU (0avgtext+0avgdata 584588maxresident)k + 486129672inputs+2998072outputs (3672major+139751796minor)pagefaults 0swaps + + => so apparently 2x tasks failed + => 1271708 = 353 hours... but what walltime? about 31-32 hours if divide by CPU + +Only received a single exception at: + + Jan 18, 2020 8:33:09 AM UTC + /srv/fatcat/datasets/pubmed_medline_baseline_2020/pubmed20n0936.xml + MalformedExternalId: 10.4149/gpb¬_2017042 + +Not sure what the other failure was... maybe an invalid filename or argument, +before processing actually started? Or some failure (OOM) that prevented sentry +reporting? + +Patch normal.py and re-run that single file: + + ./fatcat_import.py pubmed /srv/fatcat/datasets/pubmed_medline_baseline_2020/pubmed20n0936.xml /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + [...] + Counter({'total': 30000, 'exists': 27243, 'skip': 1605, 'insert': 1152, 'warn-pmid-doi-mismatch': 26, 'update': 0}) + +Done! + +## Chocula + +Command: + + export FATCAT_AUTH_WORKER_JOURNAL_METADATA=[...] + ./fatcat_import.py chocula /srv/fatcat/datasets/export_fatcat.2019-12-26.json + +Result: + + Counter({'total': 144455, 'exists': 139807, 'insert': 2384, 'skip': 2264, 'skip-unknown-new-issnl': 2264, 'exists-by-issnl': 306, 'update': 0}) diff --git a/extra/bulk_edits/2020-03-19_arxiv_pubmed.md b/extra/bulk_edits/2020-03-19_arxiv_pubmed.md new file mode 100644 index 00000000..56e88880 --- /dev/null +++ b/extra/bulk_edits/2020-03-19_arxiv_pubmed.md @@ -0,0 +1,57 @@ + +On 2020-03-20, automated daily harvesting and importing of arxiv and pubmed +metadata started. In the case of pubmed, updates are enabled, so that recently +created DOI releases get updated with PMID and extra metadata. + +We also want to do last backfills of metadata since the last import up through +the first day updated by the continuous harvester. + + +## arxiv + +The previous date span was 2019-05-22 through 2019-12-20. This time we should +do 2019-12-20 through today. + +First do metha update from last harvest through today, and grab the new daily files: + + metha-sync -format arXivRaw http://export.arxiv.org/oai2 + + mkdir arxiv_20191220_20200319 + cp 2019-12-2* 2019-12-3* 2020-* arxiv_20191220_20200319/ + tar cf arxiv_20191220_20200319.tar arxiv_20191220_20200319/ + gzip arxiv_20191220_20200319.tar + +Then copy to fatcat server and run import: + + export FATCAT_AUTH_WORKER_ARXIV=... + + ./fatcat_import.py --batch-size 100 arxiv /srv/fatcat/datasets/arxiv_20191220_20200319/2019-12-31-00000000.xml + => Counter({'exists': 1824, 'total': 1001, 'insert': 579, 'skip': 1, 'update': 0}) + + fd .xml /srv/fatcat/datasets/arxiv_20191220_20200319/ | parallel -j15 ./fatcat_import.py --batch-size 100 arxiv {} + +Ran fairly quickly only some ~80-90k entities to process. + +## PubMed + +First, mirror update files from FTP, e.g. via lftp: + + mkdir -p /srv/fatcat/datasets/pubmed_updates + lftp -e 'mirror -c /pubmed/updatefiles /srv/fatcat/datasets/pubmed_updates; bye' ftp://ftp.ncbi.nlm.nih.gov + +Inspect completed dates from kafka: + + kafkacat -b $KAFKA_BROKER -t fatcat-prod.ftp-pubmed-state -C + +Show dates and corresponding files: + + find /srv/fatcat/datasets/pubmed_updates -name "*html" | xargs cat | grep "Created" | sort + +For this bulk import, we used files pubmed20n1016.xml.gz (2019-12-16) up to pubmed20n1110.xml.gz (2020-03-06). + +To import the corresponding files, run: + + printf "%s\n" /srv/fatcat/datasets/pubmed_updates/pubmed20n{1016..1110}.xml.gz | shuf | \ + parallel -j16 'gunzip -c {} | ./fatcat_import.py pubmed --do-updates - /srv/fatcat/datasets/ISSN-to-ISSN-L.txt' + +Import took 254 min, there were 1715427 PubmedArticle docs in these update files. diff --git a/extra/bulk_edits/2020-03-23_jalc.md b/extra/bulk_edits/2020-03-23_jalc.md new file mode 100644 index 00000000..d63c3759 --- /dev/null +++ b/extra/bulk_edits/2020-03-23_jalc.md @@ -0,0 +1,23 @@ + +2019-10-01 JaLC metadata snapshot: <https://archive.org/download/jalc-bulk-metadata-2019> + +Extracted .rdf file instead of piping it through zcat. + +Use correct bot: + + export FATCAT_AUTH_WORKER_JALC=blah + +Start small; do a random bunch (10k) single-threaded to pre-create containers: + + head -n100 /srv/fatcat/datasets/JALC-LOD-20191001.rdf | ./fatcat_import.py --batch-size 100 jalc - /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + shuf -n100 /srv/fatcat/datasets/JALC-LOD-20191001.rdf | ./fatcat_import.py --batch-size 100 jalc - /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + shuf -n10000 /srv/fatcat/datasets/JALC-LOD-20191001.rdf | ./fatcat_import.py --batch-size 100 jalc - /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + +Seemed like lots of individual containers getting added after repeating, so +just going to import single-threaded to avoid duplicate container creation: + + cat /srv/fatcat/datasets/JALC-LOD-20191001.rdf | ./fatcat_import.py --batch-size 100 jalc - /srv/fatcat/datasets/ISSN-to-ISSN-L.txt + => Counter({'total': 8419745, 'exists': 6480683, 'insert': 1934082, 'skip': 4980, 'inserted.container': 134, 'update': 0}) + +Had a bit fewer than 4,568,120 "doi_registrar:jalc" releases before this +import, 6,502,202 after (based on `doi_registrar:jalc` query). diff --git a/extra/bulk_edits/2020-08-05_chocula.md b/extra/bulk_edits/2020-08-05_chocula.md new file mode 100644 index 00000000..78d2c9c3 --- /dev/null +++ b/extra/bulk_edits/2020-08-05_chocula.md @@ -0,0 +1,17 @@ + +Using `journal-metadata-bot` and `chocula_fatcat_export.2020-07-31.json` export. + +Start small: + + head -n100 /srv/fatcat/datasets/chocula_fatcat_export.2020-07-31.json | ./fatcat_import.py chocula --do-updates - + => Counter({'total': 100, 'update': 67, 'exists': 25, 'exists-skip-update': 24, 'insert': 8, 'exists-by-issnl': 1, 'skip': 0}) + +Full batch: + + time cat /srv/fatcat/datasets/chocula_fatcat_export.2020-07-31.json | ./fatcat_import.py chocula --do-updates - + + Counter({'total': 164950, 'update': 112074, 'exists': 37243, 'exists-skip-update': 35862, 'insert': 15633, 'exists-by-issnl': 1381, 'skip': 0}) + + real 16m9.779s + user 6m26.324s + sys 0m16.088s diff --git a/extra/bulk_edits/2020-09-02_file_meta.md b/extra/bulk_edits/2020-09-02_file_meta.md new file mode 100644 index 00000000..b0606f2d --- /dev/null +++ b/extra/bulk_edits/2020-09-02_file_meta.md @@ -0,0 +1,75 @@ + +Approximately 18 million file entities have only partial file metadata. All +have a sha1 (hex), but many are missing file size, md5, mimetype, etc. + +At least a few thousand of these are additionally *not* `application/pdf` +mimetype based on actually retrieving the file and sniffing the file type. +These are added earlier to the catalog likely based on CDX mimetype, which is +server-reported and can be incorrect. + +## QA Testing + + ./fatcat_import.py --editgroup-description-override "backfill of full file-level metadata for early-imported papers" file-meta - + => Counter({'total': 1000, 'update': 1000, 'skip': 0, 'insert': 0, 'exists': 0}) + + # Identical command, verifying that don't double-insert: + => Counter({'total': 1000, 'skip-existing-complete': 1000, 'skip': 0, 'insert': 0, 'update': 0, 'exists': 0}) + +Two additional file-level cleanups should probably be done at the same time: + +Partial wayback URL timestamps, for cases where we have the full timestamped URL. Eg: + + https://web.archive.org/web/2017/http://www.geoamazonia.net/index.php/revista/article/download/51/pdf_38 + https://web.archive.org/web/20170922010835/http://www.geoamazonia.net/index.php/revista/article/download/51/pdf_38 + https://qa.fatcat.wiki/file/4udmm4zd4bgfhnaaycqoztgfgm + https://qa.fatcat.wiki/file/k73il3k5hzemtnkqa5qyorg6ci + https://qa.fatcat.wiki/file/7hstlrabfjb6vgyph7ntqtpkne + +Live-web URLs identical except for http/https flip or other trivial things (much less frequent case): + + http://eo1.gsfc.nasa.gov/new/validationReport/Technology/JoeCD/asner_etal_PNAS_20041.pdf + https://eo1.gsfc.nasa.gov/new/validationReport/Technology/JoeCD/asner_etal_PNAS_20041.pdf + + http://homepages.math.uic.edu/~rosendal/PapersWebsite/BanachMinimalExamples.pdf + http://homepages.math.uic.edu:80/~rosendal/PapersWebsite/BanachMinimalExamples.pdf + https://qa.fatcat.wiki/file/h2wx6re5fjhx7c6duifzskeo6u + https://qa.fatcat.wiki/file/vw7divmjwveftn4djj2cp32n4i + +Which bot to use? Let's do `sandcrawler-bot`. + +Trying a larger batch to see what database size increase is going to look like, +and whether single-threaded is going to be too slow: + + # before: Size: 517.87G + + time zcat /srv/fatcat/datasets/fatcat_file_partial.file_meta.json.gz | head -n500000 | pv -l | ./fatcat_import.py --editgroup-description-override "backfill of full file-level metadata for early-imported papers" file-meta - + => 145m18.615s + + # after: 518.47G + # delta: 600 MB + +A million records would take about 5 hours, so 100 hours total, or 4 days. Let's do parallelism. + +Total size increase estimated as 24 GBytes. It all adds up! + + time zcat /srv/fatcat/datasets/fatcat_file_partial.file_meta.json.gz | tail -n500000 | pv -l | parallel -j8 --round-robin --pipe -q ./fatcat_import.py --editgroup-description-override 'backfill of full file-level metadata for early-imported papers' file-meta - + => real 32m53.935s + +## Production Import + +Before Size: 624.63G + + export FATCAT_API_AUTH_TOKEN... # sandcrawler-bot + + # start small + time zcat /srv/fatcat/datasets/fatcat_file_partial.file_meta.json.gz | pv -l | head -n1000 | parallel -j8 --round-robin --pipe -q ./fatcat_import.py --editgroup-description-override 'backfill of full file-level metadata for early-imported papers' file-meta - + + # full batch + time zcat /srv/fatcat/datasets/fatcat_file_partial.file_meta.json.gz | pv -l | parallel -j8 --round-robin --pipe -q ./fatcat_import.py --editgroup-description-override 'backfill of full file-level metadata for early-imported papers' file-meta - + + => 18.1M 20:53:32 [ 241 /s] + + Counter({'total': 2234159, 'update': 2234111, 'skip-existing-complete': 48, 'skip': 0, 'insert': 0, 'exists': 0}) + (etc, 8x) + +After Size: 653.69G (+29GB or so) diff --git a/extra/bulk_edits/2020-10-08_chocula.md b/extra/bulk_edits/2020-10-08_chocula.md new file mode 100644 index 00000000..d60b6842 --- /dev/null +++ b/extra/bulk_edits/2020-10-08_chocula.md @@ -0,0 +1,44 @@ + +Another update of journal metadata. In this case due to expanding "Keepers" +coverage to PKP PLN, Hathitrust, Scholar's Portal, and Carniniana. + +Using `journal-metadata-bot` and `chocula.2020-10-08.json` export. + +## QA Testing + + shuf -n1000 /srv/fatcat/datasets/chocula.2020-10-08.json | ./fatcat_import.py chocula --do-updates - + Counter({'total': 1000, 'exists': 640, 'exists-skip-update': 532, 'update': 348, 'exists-not-found': 108, 'insert': 12, 'skip': 0}) + +Expecting roughly a 1/3 update rate. Most of these seem to be true updates (eg, +adding kbart metadata). A smaller fraction are just updating DOAJ timestamp or +not updating any metadata at all. + + head -n500 /srv/fatcat/datasets/chocula.2020-10-08.json | ./fatcat_import.py chocula --do-updates - + Counter({'total': 500, 'exists': 372, 'exists-skip-update': 328, 'update': 121, 'exists-not-found': 44, 'insert': 7, 'skip': 0}) + + head -n500 /srv/fatcat/datasets/chocula.2020-10-08.json | ./fatcat_import.py chocula --do-updates - + Counter({'total': 500, 'exists': 481, 'exists-skip-update': 430, 'exists-not-found': 44, 'update': 19, 'exists-by-issnl': 7, 'skip': 0, 'insert': 0}) + +Made some changes in `27fe31d5ffcac700c30b2b10d56685ef0fa4f3a8` which seem to +have removed the spurious null updates, while retaining DOAJ date-only updates. + +Also as a small nit notice that occasionally `kbart` metadata gets added with +no year spans. This seems to be common with cariniana. Presumably this happens +when there is no year span info available, only volumes. Seems like a valuable +thing to include as a flag anyways. + +## Prod Import + +Start small: + + head -n100 /srv/fatcat/datasets/chocula.2020-10-08.json | ./fatcat_import.py chocula --do-updates - + => Counter({'total': 100, 'exists': 69, 'exists-skip-update': 68, 'update': 30, 'insert': 1, 'exists-by-issnl': 1, 'skip': 0}) + +Full batch: + + time cat /srv/fatcat/datasets/chocula.2020-10-08.json | ./fatcat_import.py chocula --do-updates - + => Counter({'total': 167092, 'exists': 110594, 'exists-skip-update': 109852, 'update': 55274, 'insert': 1224, 'exists-by-issnl': 742, 'skip': 0}) + + real 10m45.714s + user 4m51.680s + sys 0m12.236s diff --git a/extra/bulk_edits/2020-12-01_orcid.md b/extra/bulk_edits/2020-12-01_orcid.md new file mode 100644 index 00000000..b6883b17 --- /dev/null +++ b/extra/bulk_edits/2020-12-01_orcid.md @@ -0,0 +1,55 @@ + +Another annual ORCID dump, basically the same as last year (2019). Expecting +around 10 million total ORCIDs, compared to 7.3 million last year, so maybe 2.5 +million new creator entities. + +In particular motivated to run this import before a potential dblp import +and/or creator creation run. + +Files download from: + +- <https://orcid.figshare.com/articles/dataset/ORCID_Public_Data_File_2020/13066970> +- <https://archive.org/details/orcid-dump-2020> + +## Prep + + wget https://github.com/ORCID/orcid-conversion-lib/raw/master/target/orcid-conversion-lib-0.0.2-full.jar + + java -jar orcid-conversion-lib-0.0.2-full.jar --tarball -i ORCID_2020_10_summaries.tar.gz -v v3_0rc1 -o ORCID_2020_10_summaries_json.tar.gz + + tar xvf ORCID_2020_10_summaries_json.tar.gz + + fd .json ORCID_2020_10_summaries/ | parallel cat {} | jq . -c | pv -l | gzip > ORCID_2020_10_summaries.json.gz + + zcat ORCID_2020_10_summaries.json.gz | shuf -n10000 | gzip > ORCID_2020_10_summaries.sample_10k.json.gz + + ia upload orcid-dump-2020 ORCID_2020_10_summaries_json.tar.gz ORCID_2020_10_summaries.sample_10k.json.gz + +## Import + +Fetch to prod machine: + + wget https://archive.org/download/orcid-dump-2020/ORCID_2020_10_summaries.json.gz + wget https://archive.org/download/orcid-dump-2020/ORCID_2020_10_summaries.sample_10k.json.gz + +Sample: + + export FATCAT_AUTH_WORKER_ORCID=[...] + zcat /srv/fatcat/datasets/ORCID_2020_10_summaries.sample_10k.json.gz | ./fatcat_import.py orcid - + => Counter({'total': 10000, 'exists': 7356, 'insert': 2465, 'skip': 179, 'update': 0}) + +Bulk import: + + export FATCAT_AUTH_WORKER_ORCID=[...] + time zcat /srv/fatcat/datasets/ORCID_2020_10_summaries.json.gz | pv -l | parallel -j8 --round-robin --pipe ./fatcat_import.py orcid - + => Counter({'total': 1208991, 'exists': 888696, 'insert': 299008, 'skip': 21287, 'update': 0}) + => (8x of the above, roughly) + + real 88m40.960s + user 389m35.344s + sys 23m18.396s + + + Before: Size: 673.36G + After: Size: 675.55G + diff --git a/extra/bulk_edits/2020-12-14_doaj.md b/extra/bulk_edits/2020-12-14_doaj.md new file mode 100644 index 00000000..5e897183 --- /dev/null +++ b/extra/bulk_edits/2020-12-14_doaj.md @@ -0,0 +1,139 @@ + +## Earlier QA Testing (November 2020) + + export FATCAT_API_AUTH_TOKEN=... (FATCAT_AUTH_WORKER_DOAJ) + + # small test: + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13_all.json.gz | head | ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + + # full run + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13_all.json.gz | pv -l | parallel -j12 --round-robin --pipe ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + + before: 519.17G + after: 542.08G + + + 5.45M 6:29:17 [ 233 /s] + + 12x of: + Counter({'total': 455504, 'insert': 394437, 'exists': 60615, 'skip': 452, 'skip-title': 452, 'update': 0}) + + total: ~5,466,048 + insert: ~4,733,244 + exists: ~727,380 + +Initial imports (before crash) were like: + + Counter({'total': 9339, 'insert': 9330, 'skip': 9, 'skip-title': 9, 'update': 0, 'exists': 0}) + +Seems like there is a bug, not finding existing by DOI? + +## Prod Container Metadata Update (chocula) + +Generic update of container metadata using chocula pipeline. Need to run this +before DOAJ import to ensure we have all the containers already updated. + +Also updating ISSN-L index at the same time. Using a 2020-11-19 metadata +snapshot, which was generated on 2020-12-07; more recent snapshots had small +upstream changes in some formats so it wasn't trivial to run with a newer +snapshot. + + # git rev: 9f67c82ce8952bbe9a7a07b732830363c7865485 + + # from laptop, then unzip on prod machine + scp chocula_fatcat_export.2020-11-19.json.gz fatcat-prod1-vm:/srv/fatcat/datasets/ + + # check ISSN-L symlink + # ISSN-to-ISSN-L.txt -> 20201119.ISSN-to-ISSN-L.txt + + export FATCAT_AUTH_WORKER_JOURNAL_METADATA=... + head -n200 /srv/fatcat/datasets/chocula_fatcat_export.2020-11-19.json | ./fatcat_import.py chocula - + Counter({'total': 200, 'exists': 200, 'exists-by-issnl': 6, 'skip': 0, 'insert': 0, 'update': 0}) + + head -n200 /srv/fatcat/datasets/chocula_fatcat_export.2020-11-19.json | ./fatcat_import.py chocula - --do-updates + Counter({'total': 200, 'exists': 157, 'exists-skip-update': 151, 'update': 43, 'exists-by-issnl': 6, 'skip': 0, 'insert': 0}) + +Some of these are very minor updates, so going to do just creation (no +`--do-updates`) to start. + + time ./fatcat_import.py chocula /srv/fatcat/datasets/chocula_fatcat_export.2020-11-19.json + Counter({'total': 168165, 'exists': 167497, 'exists-by-issnl': 2371, 'insert': 668, 'skip': 0, 'update': 0}) + + real 5m37.081s + user 3m1.648s + sys 0m9.488s + +TODO: tweak chocula import script to not update on `extra.state` metadata. + + +## Release Metadata Bulk Import + +This is the first production bulk import of DOAJ metadata! + + # git rev: 9f67c82ce8952bbe9a7a07b732830363c7865485 + # DB before: Size: 678.15G + + # ensure fatcatd is updated to have support for DOAJ identifier + + # create new bot user + ./target/release/fatcat-auth create-editor --admin --bot doaj-bot + => mir5imb3v5ctxcaqnbstvmri2a + + ./target/release/fatcat-auth create-token mir5imb3v5ctxcaqnbstvmri2a + => ... + + # download dataset + wget https://archive.org/download/doaj_data_2020-11-13/doaj_article_data_2020-11-13.sample_10k.json.gz + wget https://archive.org/download/doaj_data_2020-11-13/doaj_article_data_2020-11-13_all.json.gz + + export FATCAT_AUTH_WORKER_DOAJ=... + + # start small + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13.sample_10k.json.gz | head -n100 | ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + => Counter({'total': 100, 'exists': 70, 'insert': 30, 'skip': 0, 'update': 0}) + +That is about expected, in terms of fraction without DOI. However, 6 out of 10 +(randomly checked) of the inserted releases seem to be dupes, which feels too +high. So going to pause this import until basic fuzzy matching ready from +Martin's fuzzycat work, and will check against elasticsearch before import. +Will shuffle the entire file, import in a single thread, and just skip +importing if there is any fuzzy match (not try to merge/update). Expecting +about 500k new releases after such filtering. + +Ok, on 2020-12-17, back with patches to use fuzzycat in filtering. Trying +another batch: + + # git rev: 60e022609cd3fbbf9634577149018592e680858d + # DB before: Size: 678.47G + + export FATCAT_AUTH_WORKER_DOAJ=... + + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13.sample_10k.json.gz | head -n1000 | tail -n100 | ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + => Counter({'total': 100, 'exists': 71, 'insert': 19, 'exists-fuzzy': 10, 'skip': 0, 'update': 0}) + + # https://fatcat.wiki/changelog/5033496 + +Sampled 10x of these and they look much better: no obvious duplication. Going +ahead with the full import; note that other ingest is happening in parallel +(many crossref, datacite, and pubmed imports which backed up). + + # full run + # note the shuf command added, in an attempt to reduce duplicates within this corpus + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13_all.json.gz | shuf | pv -l | parallel -j12 --round-robin --pipe ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + + # started 2020-12-17 22:01 (Pacific) + + => 5.45M 52:38:45 [28.8 /s] + => Counter({'total': 1366458, 'exists': 1020295, 'insert': 200249, 'exists-fuzzy': 144334, 'skip': 1563, 'skip-title': 1563, 'skip-doaj-id-mismatch': 17, 'update': 0}) + +As total estimates: + +- total: 5,465,832 +- exists: 4,081,180 +- exists-fuzzy: 577,336 +- insert: 800,996 + +Ending database size: Size: 684.08G + +(note that regular imports were running during same period) + diff --git a/extra/bulk_edits/2020-12-23_dblp.md b/extra/bulk_edits/2020-12-23_dblp.md new file mode 100644 index 00000000..a33411cb --- /dev/null +++ b/extra/bulk_edits/2020-12-23_dblp.md @@ -0,0 +1,55 @@ + +## Prod Container Import + +Using 2020-11-30 XML dump, then scrape and transform tooling from +`extra/dblp/`. + + wget https://archive.org/download/dblp-xml-2020-11-30/dblp_container_meta.json + + # updated ISSN-to-ISSN-L.txt symlink to 20201207.ISSN-to-ISSN-L.txt + + touch /srv/fatcat/datasets/blank_dblp_containers.tsv + +Create new `dblp-bot` user: + + ./target/release/fatcat-auth create-editor --admin --bot dblp-bot + => gwbheb5jfngrxkcad5qgth5cra + + ./target/release/fatcat-auth create-token gwbheb5jfngrxkcad5qgth5cra + +Run import: + + # git commit: ec6b366af8df1956e1287cba2e0818b80ce1c518 + + export FATCAT_AUTH_WORKER_DBLP=... + + ./fatcat_import.py dblp-container --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt --dblp-container-map-file /srv/fatcat/datasets/blank_dblp_containers.tsv --dblp-container-map-output /srv/fatcat/datasets/all_dblp_containers.tsv /srv/fatcat/datasets/dblp_container_meta.json + => Got 0 existing dblp container mappings. + => Counter({'total': 6954, 'insert': 5202, 'exists': 1752, 'skip': 0, 'update': 0}) + + wc -l /srv/fatcat/datasets/all_dblp_containers.tsv + 6955 /srv/fatcat/datasets/all_dblp_containers.tsv + +## Prod Release Import + +Using same 2020-11-30 XML dump. Download to /srv/fatcat/datasets: + + wget https://archive.org/download/dblp-xml-2020-11-30/dblp.dtd + wget https://archive.org/download/dblp-xml-2020-11-30/dblp.xml + +Run import: + + export FATCAT_AUTH_WORKER_DBLP=... + + ./fatcat_import.py dblp-release --dblp-container-map-file /srv/fatcat/datasets/all_dblp_containers.tsv /srv/fatcat/datasets/dblp.xml --do-updates + + # started 2020-12-23 11:51 (Pacific) + + # restarted/tweaked at least twice + + # finally ended around 2020-12-27 after about... 48 hours? + + => Counter({'total': 7953365, 'has-doi': 4277307, 'skip': 3097418, 'skip-key-type': 2640968, 'skip-update': 2480449, 'exists': 943800, 'update': 889700, 'insert': 338842, 'skip-arxiv-corr': 312872, 'exists-fuzzy': 203103, 'skip-dblp-container-missing': 143578, 'skip-arxiv': 53, 'skip-title': 1}) + +Starting database size (roughly): Size: 684.08G +Ending database size: Size: 690.22G diff --git a/extra/bulk_edits/2020_datacite.md b/extra/bulk_edits/2020_datacite.md new file mode 100644 index 00000000..05d09517 --- /dev/null +++ b/extra/bulk_edits/2020_datacite.md @@ -0,0 +1,152 @@ + + +## QA Runs + +Trying on 2019-12-22, using Martin commit 18d411087007a30fbf027b87e30de42344119f0c from 2019-12-20. + +Quick test: + + # this branch adds some new deps, so make sure to install them + pipenv install --deploy --dev + pipenv shell + export FATCAT_AUTH_WORKER_DATACITE="..." + xzcat /srv/fatcat/datasets/datacite.ndjson.xz | head -n100 | ./fatcat_import.py datacite - /srv/fatcat/datasets/20181203.ISSN-to-ISSN-L.txt --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3 + +ISSUE: `--extid-map-file` not passed through, so drop the: + + --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3 + +ISSUE: auth_var should be FATCAT_AUTH_WORKER_DATACITE + +Test full parallel command: + + export FATCAT_AUTH_WORKER_DATACITE="..." + time xzcat /srv/fatcat/datasets/datacite.ndjson.xz | head -n10000 | parallel -j20 --round-robin --pipe ./fatcat_import.py datacite - /srv/fatcat/datasets/20181203.ISSN-to-ISSN-L.txt --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3 + + real 0m30.017s + user 3m5.576s + sys 0m19.640s + +Whole lot of: + + invalid literal for int() with base 10: '10,495' + invalid literal for int() with base 10: '11,129' + + invalid literal for int() with base 10: 'n/a' + invalid literal for int() with base 10: 'n/a' + + invalid literal for int() with base 10: 'OP98' + invalid literal for int() with base 10: 'OP208' + + no mapped type: None + no mapped type: None + no mapped type: None + +Re-ran above: + + real 0m27.764s + user 3m2.448s + sys 0m12.908s + +Compare with `--lang-detect`: + + real 0m27.395s + user 3m5.620s + sys 0m13.344s + +Not noticeable? + +Whole run: + + export FATCAT_AUTH_WORKER_DATACITE="..." + time xzcat /srv/fatcat/datasets/datacite.ndjson.xz | parallel -j20 --round-robin --pipe ./fatcat_import.py datacite - /srv/fatcat/datasets/20181203.ISSN-to-ISSN-L.txt --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3 + + real 35m21.051s + user 98m57.448s + sys 7m9.416s + +Huh. Kind of suspiciously fast. + + select count(*) from editgroup where editor_id='07445cd2-cab2-4da5-9f84-34588b7296aa'; + => 9952 editgroups + + select count(*) from release_edit inner join editgroup on release_edit.editgroup_id = editgroup.id where editgroup.editor_id='07445cd2-cab2-4da5-9f84-34588b7296aa'; + => 496,342 edits + +While running: + + starting around 5k TPS in pg_activity + starting size: 367.58G + (this is after arxiv and some other changes on top of 2019-12-13 dump) + host doing a load average of about 5.5; fatcatd at 115% CPU + + ending size: 371.43G + +Actually seems like extremely few DOIs getting inserted? Hrm. + + xzcat /srv/fatcat/datasets/datacite.ndjson.xz | wc -l + => 18,210,075 + +Last DOIs inserted were around: 10.7916/d81v6rqr + +Suspect a bunch of errors or something and output getting mangled by all the +logging? Squelched logging and running again (using same DB/config), except +with `pv -l` inserted after `xzcat`. + +Seem to run at a couple hundred records a second (very volatile). + + Counter({'total': 42919, 'insert': 21579, 'exists': 21334, 'skip': 6, 'skip-blank-title': 6, 'inserted.container': 1, 'update': 0}) + Counter({'total': 43396, 'insert': 23274, 'exists': 20120, 'skip-blank-title': 2, 'skip': 2, 'update': 0}) + +Ok! The actual errors: + + + Traceback (most recent call last): + File "./fatcat_import.py", line 507, in <module> + main() + File "./fatcat_import.py", line 504, in main + args.func(args) + File "./fatcat_import.py", line 182, in run_datacite + JsonLinePusher(dci, args.json_file).run() + File "/srv/fatcat/src/python/fatcat_tools/importers/common.py", line 559, in run + self.importer.push_record(record) + File "/srv/fatcat/src/python/fatcat_tools/importers/common.py", line 318, in push_record + entity = self.parse_record(raw_record) + File "/srv/fatcat/src/python/fatcat_tools/importers/datacite.py", line 447, in parse_record + sha1 = hashlib.sha1(text.encode('utf-8')).hexdigest() + AttributeError: 'list' object has no attribute 'encode' + + fatcat_openapi_client.exceptions.ApiException: (400) + Reason: Bad Request + HTTP response headers: HTTPHeaderDict({'Content-Length': '186', 'Content-Type': 'application/json', 'Date': 'Mon, 23 Dec 2019 08:12:16 GMT', 'X-Clacks-Overhead': 'GNU aaronsw, jpb', 'X-Span-ID': '73b0b698-bf88-4721-b869-b322dbe90cbe'}) + HTTP response body: {"success":false,"error":"MalformedExternalId","message":"external identifier doesn't match required pattern for a DOI (expected, eg, '10.1234/aksjdfh'): 10.17167/mksz.2017.2.129–155"} + + + Traceback (most recent call last): + File "./fatcat_import.py", line 507, in <module> + main() + File "./fatcat_import.py", line 504, in main + args.func(args) + File "./fatcat_import.py", line 182, in run_datacite + JsonLinePusher(dci, args.json_file).run() + File "/srv/fatcat/src/python/fatcat_tools/importers/common.py", line 559, in run + self.importer.push_record(record) + File "/srv/fatcat/src/python/fatcat_tools/importers/common.py", line 318, in push_record + entity = self.parse_record(raw_record) + File "/srv/fatcat/src/python/fatcat_tools/importers/datacite.py", line 447, in parse_record + sha1 = hashlib.sha1(text.encode('utf-8')).hexdigest() + AttributeError: 'list' object has no attribute 'encode' + + + fatcat_openapi_client.exceptions.ApiException: (400) + Reason: Bad Request + HTTP response headers: HTTPHeaderDict({'Content-Type': 'application/json', 'X-Span-ID': 'ca141ff4-83f7-4ee5-9256-91b23ec09e94', 'Content-Length': '188', 'X-Clacks-Overhead': 'GNU aaronsw, jpb', 'Date': 'Mon, 23 Dec 2019 08:11:25 GMT'}) + HTTP response body: {"success":false,"error":"ConstraintViolation","message":"unexpected database error: new row for relation \"release_contrib\" violates check constraint \"release_contrib_raw_name_check\""} + +## Prod Import + +Around first/second week of january. Needed to restart at least once due to +database deadlock on abstract inserts, which seems to be due to parallelism and +duplicated records in the bulk datacite dump. + +TODO: specific command used by martin diff --git a/extra/bulk_edits/2021-05-28_dblp.md b/extra/bulk_edits/2021-05-28_dblp.md new file mode 100644 index 00000000..061f4f45 --- /dev/null +++ b/extra/bulk_edits/2021-05-28_dblp.md @@ -0,0 +1,44 @@ + +## Container Import + +Following dblp README directions: + + export DBLP_DIR=/srv/fatcat/tasks/202105_dblp + + ./fatcat_import.py dblp-release $DBLP_DIR/dblp.xml --dump-json-mode | pv -l > $DBLP_DIR/dblp_releases.json + => Counter({'total': 8328073, 'skip': 8328073, 'has-doi': 4478439, 'skip-key-type': 2764750, 'skip-arxiv-corr': 348766, 'skip-title': 1, 'insert': 0, 'update': 0, 'exists': 0}) + => 5.21M 3:38:35 [ 397 /s] + + cat $DBLP_DIR/dblp_releases.json | jq ._dblp_prefix -r | grep -v ^null | sort -u > $DBLP_DIR/prefix_list.txt + + wc -l $DBLP_DIR/prefix_list.txt + => 7603 /srv/fatcat/tasks/202105_dblp/prefix_list.txt + + mkdir -p journals + mkdir -p conf + mkdir -p series + + shuf $DBLP_DIR/prefix_list.txt | pv -l | parallel -j1 wget -nc -q "https://dblp.org/db/{}/index.html" -O {}.html + + # switch to temporary selectolax pipenv + fd html conf/ journals/ series/ | /srv/fatcat/src/extra/dblp/dblp_html_extract.py | pv -l > dblp_container_meta.json + => 7.08k 0:00:15 [ 449 /s] + + fatcat-cli search containers dblp_prefix:* -n 0 --index-json | jq "[.dblp_prefix, .ident] | @tsv" -r | pv -l > existing_dblp_containers.tsv + => Got 5202 hits in 47ms + => 5.20k 0:00:13 [ 375 /s] + + ./fatcat_import.py dblp-container --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt --dblp-container-map-file $DBLP_DIR/existing_dblp_containers.tsv --dblp-container-map-output $DBLP_DIR/all_dblp_containers.tsv $DBLP_DIR/dblp_container_meta.json + => Counter({'total': 7083, 'exists': 7025, 'insert': 58, 'skip': 0, 'update': 0}) + => actually 108 inserted + +Actually imported 50 more before this, then Ctrl-C to check. Then re-did +fatcat-cli query, upload, and re-ran all. So 108 new containers inserted. + +## Release Import + +With same exports as above: + + ./fatcat_import.py dblp-release --dblp-container-map-file $DBLP_DIR/all_dblp_containers.tsv $DBLP_DIR/dblp.xml + => Counter({'total': 8328073, 'exists': 4847353, 'has-doi': 4478439, 'skip': 3259925, 'skip-key-type': 2764750, 'skip-arxiv-corr': 348766, 'exists-fuzzy': 202880, 'skip-dblp-container-missing': 146408, 'insert': 17862, 'skip-arxiv': 53, 'skip-title': 1, 'update': 0}) + diff --git a/extra/bulk_edits/2021-05-28_doaj.md b/extra/bulk_edits/2021-05-28_doaj.md new file mode 100644 index 00000000..e5925eeb --- /dev/null +++ b/extra/bulk_edits/2021-05-28_doaj.md @@ -0,0 +1,80 @@ + +Note: running 2021-05-28 pacific time, but 2021-05-29 UTC. + +First downloaded bulk metadata from doaj.org and uploaded into archive.org item +as a snapshot. + +## Journal Metadata Import + +Before doing article import, want to ensure journals all exist. + +Use chocula pipeline, and to be simple/conservative don't update any +containers, just create if they don't already exist. + +Run the usual chocula source update, copy to data dir, update sources.toml, +etc. Didn't bother with updating container counts or homepage status. Then +export container schema: + + python -m chocula export_fatcat | gzip > chocula_fatcat_export.2021-05-28.json.gz + +Upload to fatcat prod machine, unzip, and then import to prod: + + export FATCAT_AUTH_WORKER_JOURNAL_METADATA=[...] + ./fatcat_import.py chocula /srv/fatcat/datasets/chocula_fatcat_export.2021-05-28.json + => Counter({'total': 175837, 'exists': 170358, 'insert': 5479, 'exists-by-issnl': 5232, 'skip': 0, 'update': 0}) + +That is a healthy batch of new records! + +## Article Import + +Transform all the articles into a single JSON file: + + cat doaj_article_data_*/article_batch*.json | jq .[] -c | pv -l | gzip > doaj_article_data_2021-05-25_all.json.gz + => 6.1M 0:18:45 [5.42k/s] + + zcat doaj_article_data_2021-05-25_all.json.gz | shuf -n10000 > doaj_article_data_2021-05-25_sample_10k.json + +Also upload this `_all` file to archive.org item. + +Ready to import! Start with sample: + + export FATCAT_AUTH_WORKER_DOAJ=... + zcat /srv/fatcat/tasks/202105_doaj/doaj_article_data_2021-05-25_sample_10k.json.gz | ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + => Counter({'total': 10000, 'exists': 8743, 'exists-fuzzy': 1044, 'insert': 197, 'skip': 14, 'skip-title': 14, 'skip-doaj-id-mismatch': 2, 'update': 0}) + +Then the full import, in parallel, shuffled (because we shuffled last time): + + zcat /srv/fatcat/tasks/202105_doaj/doaj_article_data_2021-05-25_all.json.gz | shuf | pv -l | parallel -j12 --round-robin --pipe ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + => Counter({'total': 512351, 'exists': 449996, 'exists-fuzzy': 50858, 'insert': 10826, 'skip': 551, 'skip-title': 551, 'skip-doaj-id-mismatch': 120, 'update': 0}) + => extrapolating, about 129,912 new release entities. 2.1% insert rate + +NOTE: large number of warnings like: + + UserWarning: unexpected DOAJ ext_id match after lookup failed doaj=5d2ebb760ad24ce68ec8079bc82c8d78 ident=dvtl2xpn4nespfrj6gad6mrk44 + +## Extra Article Imports + +Manually disabled fuzzy matching with patch: + + diff --git a/python/fatcat_import.py b/python/fatcat_import.py + index 1dcfec2..cb787cb 100755 + --- a/python/fatcat_import.py + +++ b/python/fatcat_import.py + @@ -260,6 +260,7 @@ def run_doaj_article(args): + args.issn_map_file, + edit_batch_size=args.batch_size, + do_updates=args.do_updates, + + do_fuzzy_match=False, + ) + if args.kafka_mode: + KafkaJsonPusher( + +Filtered out some specific articles: + + zcat doaj_article_data_2021-05-25_all.json.gz | rg 1665-1596 | pv -l > doaj_article_data_2021-05-25_voces.json + => 154 0:02:05 [1.22 /s] + +And used this for some imports: + + cat /srv/fatcat/tasks/202105_doaj/doaj_article_data_2021-05-25_voces.json | ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + diff --git a/extra/bulk_edits/2021-11-10_case_sensitive_dois.md b/extra/bulk_edits/2021-11-10_case_sensitive_dois.md new file mode 100644 index 00000000..20772f56 --- /dev/null +++ b/extra/bulk_edits/2021-11-10_case_sensitive_dois.md @@ -0,0 +1,53 @@ + +## Production Run + +Start small: + + export FATCAT_AUTH_WORKER_CLEANUP=[...] + + wc -l /srv/fatcat/datasets/nonlowercase_doi_releases.tsv + # 140530 + + head -n100 /srv/fatcat/datasets/nonlowercase_doi_releases.tsv \ + | python -m fatcat_tools.cleanups.release_lowercase_doi - + # Counter({'total': 100, 'update': 100, 'skip': 0, 'insert': 0, 'exists': 0}) + + # same command again to test not duping updates + Counter({'total': 100, 'skip-existing-doi-fine': 100, 'skip': 0, 'insert': 0, 'update': 0, 'exists': 0}) + + # example editgroup_cld5qe34bzg7xg7g4cz5skgaw4 + +Database size just before, while some other edits happening, PostgreSQL 11.6: 762.66G + +Ok, run a bunch in parallel: + + cat /srv/fatcat/datasets/nonlowercase_doi_releases.tsv \ + | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.release_lowercase_doi - + # Counter({'total': 24022, 'update': 24022, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 38836, 'update': 38836, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 38836, 'update': 38836, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 38836, 'update': 38736, 'skip-existing-doi-fine': 100, 'skip': 0, 'insert': 0, 'exists': 0}) + +Over 3k TPS in `pg_activity`. + +Should have included `pv -l` in the pipeline. + +Final database size 763.14G, so only a couple hundred MByte of growth, totally +fine. + + +## Verification + +Re-dump release extids, in production: + + sudo -u postgres psql fatcat_prod < dump_release_extid.sql | egrep -v ^BEGIN$ | egrep -v ^ROLLBACK$ | pv -l | pigz > /srv/fatcat/snapshots/release_extid.tsv.gz + +Filter to non-lowercase DOIs: + + zcat release_extid.tsv.gz \ + | cut -f1,3 \ + | rg '[A-Z]' \ + | pv -l \ + > nonlowercase_doi.tsv + +Zero returned, hurray! diff --git a/extra/bulk_edits/2021-11-10_file_release_ingest_bugfix.md b/extra/bulk_edits/2021-11-10_file_release_ingest_bugfix.md new file mode 100644 index 00000000..6b5deb63 --- /dev/null +++ b/extra/bulk_edits/2021-11-10_file_release_ingest_bugfix.md @@ -0,0 +1,108 @@ + +## Production Run + +Start small: + + export FATCAT_AUTH_WORKER_CLEANUP=[...] + + wc -l /srv/fatcat/datasets/file_release_bugfix_20211105.json + 228826 + + head -n100 /srv/fatcat/datasets/file_release_bugfix_20211105.json \ + | python -m fatcat_tools.cleanups.file_release_bugfix - + # Counter({'total': 100, 'update': 100, 'skip': 0, 'insert': 0, 'exists': 0}) + + # example editgroup_keae3rfekffuriiy77f26rf6uq + +These are all now stubs (no release associated), which isn't the ratio seen in QA. Going to do a random sample: + + shuf -n100 /srv/fatcat/datasets/file_release_bugfix_20211105.json \ + | python -m fatcat_tools.cleanups.file_release_bugfix - + # Counter({'total': 100, 'update': 100, 'skip': 0, 'insert': 0, 'exists': 0}) + + # example editgroup_34mk525kxvdu3hak7g7fr7awru + +Looked at a few and all looked more like what would be expected, correct matches. + +Comparing before and after counts is going to be tricky, and will require a +full re-index for an accurate count. But did do a snapshot just before this run +(2021-11-10-prod-stats.json), and got 31,110,184 `in_web`. + +Full edit, in parallel: + + cat /srv/fatcat/datasets/file_release_bugfix_20211105.json \ + | pv -l \ + | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.file_release_bugfix - + # 228k 0:26:34 [ 143 /s] + # Counter({'total': 26090, 'update': 26071, 'skip-existing-fixed': 15, 'skip': 4, 'skip-wrong-release-is-ok': 4, 'insert': 0, 'exists': 0}) + # Counter({'total': 26080, 'update': 26061, 'skip-existing-fixed': 12, 'skip': 7, 'skip-wrong-release-is-ok': 7, 'insert': 0, 'exists': 0}) + # Counter({'total': 27517, 'update': 27497, 'skip-existing-fixed': 15, 'skip': 5, 'skip-wrong-release-is-ok': 5, 'insert': 0, 'exists': 0}) + # Counter({'total': 29534, 'update': 29420, 'skip-existing-fixed': 110, 'skip': 4, 'skip-wrong-release-is-ok': 4, 'insert': 0, 'exists': 0}) + # Counter({'total': 29544, 'update': 29517, 'skip-existing-fixed': 16, 'skip': 11, 'skip-wrong-release-is-ok': 11, 'insert': 0, 'exists': 0}) + # Counter({'total': 29535, 'update': 29518, 'skip-existing-fixed': 10, 'skip': 7, 'skip-wrong-release-is-ok': 7, 'insert': 0, 'exists': 0}) + # Counter({'total': 30082, 'update': 30065, 'skip-existing-fixed': 13, 'skip': 4, 'skip-wrong-release-is-ok': 4, 'insert': 0, 'exists': 0}) + # Counter({'total': 30444, 'update': 30420, 'skip-existing-fixed': 21, 'skip': 3, 'skip-wrong-release-is-ok': 3, 'insert': 0, 'exists': 0}) + +## Verification + +Counts: + + SELECT file_edit.extra_json->>'ingest_request_source' as source, COUNT(*) as broken_files + FROM file_edit + LEFT JOIN file_ident ON file_edit.ident_id = file_ident.id + 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 lower(release_rev.doi) != lower(file_edit.extra_json->>'link_source_id') + AND file_ident.rev_id = file_edit.rev_id + GROUP BY file_edit.extra_json->>'ingest_request_source'; + + source | broken_files + -----------+-------------- + unpaywall | 233 + (1 row) + +Examples: + + 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_ident ON file_edit.ident_id = file_ident.id + 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 lower(release_rev.doi) != lower(file_edit.extra_json->>'link_source_id') + AND file_ident.rev_id = file_edit.rev_id + LIMIT 20; + + +Looks like many of the remaining mismatches are from "double-slash" normalization, with doi prefix 10.1037: + + file_ident | release_ident | file_edit_doi | release_doi + --------------------------------------+--------------------------------------+------------------------------+------------------------------ + ae2f7864-66a6-4a82-a0e6-153cb4d0b03a | 0f436ae6-d7b4-4a45-a434-d158bc4a3437 | 10.1037/0096-1523.25.6.1568 | 10.1037//0096-1523.25.6.1568 + d02ff5ab-a882-4a86-8a94-ce6222708323 | 2d5ebbca-e4ba-4bb7-bb19-f1e081479eab | 10.1037//0021-9010.63.4.467 | 10.1037/0021-9010.63.4.467 + 2c107387-f57f-4855-bc1a-e40704f1e9b4 | 7654b956-4776-4f6f-bc35-ccf7e6bfe99c | 10.1037/0022-0663.75.4.500 | 10.1037//0022-0663.75.4.500 + 15e3636a-4bcf-4595-8a2a-b6b06a299a2f | c09e3531-1ac4-4bfa-9fcf-8acb9f0d845e | 10.1037//1064-1297.8.2.225 | 10.1037/1064-1297.8.2.225 + dc8b86c8-9b8e-4333-abbb-8811010d9c71 | bd91e7be-c360-47af-a634-f048e2c85b73 | 10.1037//0021-843x.105.4.637 | 10.1037/0021-843x.105.4.637 + 35a06e0a-6f72-4624-87ca-fbb74bc9d77d | 96befa26-6eb0-47c0-a0ec-e00282e33bff | 10.1037//0735-7044.99.5.964 | 10.1037/0735-7044.99.5.964 + 707bfaa1-65de-4dbb-9786-51b99d03d91d | 2d58524b-4216-4092-8ddf-336ac42d5955 | 10.1037/0096-1523.28.3.515 | 10.1037//0096-1523.28.3.515 + de9ea98f-672e-44ec-9d12-e11acd8990d0 | 20f1a857-ad51-4b80-9ce5-bc3a44df96b1 | 10.1037//0002-9432.71.1.72 | 10.1037/0002-9432.71.1.72 + 4275306c-11ef-4fce-bc03-3f1efe99f9a6 | c69bc740-4da1-4f96-acc9-151a0cef5c3f | 10.1037//1064-1297.6.1.107 | 10.1037/1064-1297.6.1.107 + 6a63d2ae-b953-48ba-a68a-061543d82ad4 | e3c8b8c1-defc-44ac-8c73-e21e8cf93f5c | 10.1037//0022-0167.23.6.557 | 10.1037/0022-0167.23.6.557 + 2fcbb54e-8fa8-4bbc-a2ae-4b6b6eaff412 | 8500b4a5-a693-4415-b4a4-4dcfb3403d82 | 10.1037/0021-9010.73.1.68 | 10.1037//0021-9010.73.1.68 + b9aa4601-4a1b-4146-aa6b-a410d0fc3dce | 954f2072-8c53-41c7-82b0-8c6fe9ef4d0c | 10.1037//0278-6133.13.4.319 | 10.1037/0278-6133.13.4.319 + b528b924-0680-43f3-81ad-d822e51b3373 | 69387969-40bc-451d-b567-8713296f60b0 | 10.1037//0002-9432.71.1.38 | 10.1037/0002-9432.71.1.38 + f64f1ee2-b787-4a06-87ab-46b94f9d5454 | c082d47f-175d-456a-a741-650b5eaa5173 | 10.1037//0021-843x.98.4.487 | 10.1037/0021-843x.98.4.487 + 86e8b655-963a-4c11-ae70-a8d528400682 | 6381254c-e339-4354-b0d8-711b5b5e4fcc | 10.1037/0022-0663.89.1.183 | 10.1037//0022-0663.89.1.183 + 716e1761-8120-480b-b096-e7698c65456a | 7a4d2c7d-32b7-4292-adbf-b791387a3ac5 | 10.1037//0278-7393.21.5.1209 | 10.1037/0278-7393.21.5.1209 + bb7aa131-d5e5-497e-8040-b1729850b94c | 1ce29f33-d020-4d5f-a8b3-2b8bef53ccb8 | 10.1037//1040-3590.7.4.533 | 10.1037/1040-3590.7.4.533 + 510ad392-43aa-42dc-9644-9697f425efd5 | 796c92ca-767a-495b-ad0c-f458381c071c | 10.1037//0278-7393.20.4.824 | 10.1037/0278-7393.20.4.824 + 32c57e68-0793-4ded-bca2-d05f3532ff3e | 1567a003-0b5a-48bb-bb7c-7dff2c44b90b | 10.1037//1040-3590.13.1.59 | 10.1037/1040-3590.13.1.59 + e0d1fd38-17d8-42ac-b9df-60312829ddd4 | 0cefaf5d-fcdf-4049-a9d7-0c569096478e | 10.1037//0022-006x.56.4.621 | 10.1037/0022-006x.56.4.621 + (20 rows) diff --git a/extra/bulk_edits/2021-11-11_wayback_short_ts.md b/extra/bulk_edits/2021-11-11_wayback_short_ts.md new file mode 100644 index 00000000..20349f0c --- /dev/null +++ b/extra/bulk_edits/2021-11-11_wayback_short_ts.md @@ -0,0 +1,52 @@ + +## Production Run + +At git commit `6ad9d24e4d7d901d6fc394e6e91575f6acba7ff4`. + +Start small: + + export FATCAT_AUTH_WORKER_CLEANUP=[...] + + zcat /srv/fatcat/datasets/files_20211105_moreshortts.fetched.json.gz \ + | head -n100 \ + | python -m fatcat_tools.cleanups.file_short_wayback_ts - + # Counter({'total': 100, 'update': 99, 'skip-bad-wayback-timestamp': 1, 'skip': 0, 'insert': 0, 'exists': 0}) + +Looks good! Run the full batch. + + zcat /srv/fatcat/datasets/files_20211105_moreshortts.fetched.json.gz \ + | pv -l \ + | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.file_short_wayback_ts - + + [...] + bad replacement URL: partial_ts=2017 original=https://www.hydrol-earth-syst-sci.net/21/4959/2017/hess-21-4959-2017.pdf fix_url=https://web.archive.org/web/20180721004954/https://www.hydrol-earth-syst-sci.net/21/4959/2017/hess-21-4959-2017.pdf + bad replacement URL: partial_ts=2017 original=https://www.the-cryosphere.net/11/1537/2017/tc-11-1537-2017.pdf fix_url=https://web.archive.org/web/20180719235703/https://www.the-cryosphere.net/11/1537/2017/tc-11-1537-2017.pdf + bad replacement URL: partial_ts=2017 original=http://www.growingscience.com/msl/Vol7/msl_2017_26.pdf fix_url=https://web.archive.org/web/20180601235059/http://www.growingscience.com/msl/Vol7/msl_2017_26.pdf + bad replacement URL: partial_ts=2017 original=https://www.hydrol-earth-syst-sci.net/21/4115/2017/hess-21-4115-2017.pdf fix_url=https://web.archive.org/web/20180719162956/https://www.hydrol-earth-syst-sci.net/21/4115/2017/hess-21-4115-2017.pdf + bad replacement URL: partial_ts=2017 original=https://www.biogeosciences.net/14/4279/2017/bg-14-4279-2017.pdf fix_url=https://web.archive.org/web/20180720220056/https://www.biogeosciences.net/14/4279/2017/bg-14-4279-2017.pdf + bad replacement URL: partial_ts=2017 original=https://www.biogeosciences.net/14/3669/2017/bg-14-3669-2017.pdf fix_url=https://web.archive.org/web/20180720222828/https://www.biogeosciences.net/14/3669/2017/bg-14-3669-2017.pdf + [...] + bad replacement URL: partial_ts=2017 original=http://www.growingscience.com/msl/Vol7/msl_2017_28.pdf fix_url=https://web.archive.org/web/20180602071632/http://www.growingscience.com/msl/Vol7/msl_2017_28.pdf + bad replacement URL: partial_ts=2017 original=https://www.biogeosciences.net/14/4161/2017/bg-14-4161-2017.pdf fix_url=https://web.archive.org/web/20180720004438/https://www.biogeosciences.net/14/4161/2017/bg-14-4161-2017.pdf + bad replacement URL: partial_ts=2017 original=https://core.ac.uk/download/pdf/10915563.pdf fix_url=https://web.archive.org/web/20190220174144/https://core.ac.uk/download/pdf/10915563.pdf + bad replacement URL: partial_ts=2017 original=http://www.growingscience.com/ijiec/Vol9/IJIEC_2017_24.pdf fix_url=https://web.archive.org/web/20180602094300/http://www.growingscience.com/ijiec/Vol9/IJIEC_2017_24.pdf + bad replacement URL: partial_ts=2017 original=https://core.ac.uk/download/pdf/36046645.pdf fix_url=https://web.archive.org/web/20190220175351/https://core.ac.uk/download/pdf/36046645.pdf + bad replacement URL: partial_ts=2017 original=https://core.ac.uk/download/pdf/35085886.pdf fix_url=https://web.archive.org/web/20190220175410/https://core.ac.uk/download/pdf/35085886.pdf + bad replacement URL: partial_ts=2017 original=https://www.atmos-chem-phys.net/17/10349/2017/acp-17-10349-2017.pdf fix_url=https://web.archive.org/web/20181102190649/https://www.atmos-chem-phys.net/17/10349/2017/acp-17-10349-2017.pdf + bad replacement URL: partial_ts=2017 original=https://www.atmos-chem-phys.net/17/7775/2017/acp-17-7775-2017.pdf fix_url=https://web.archive.org/web/20181101041355/https://www.atmos-chem-phys.net/17/7775/2017/acp-17-7775-2017.pdf + bad replacement URL: partial_ts=2017 original=http://www.veterinaryworld.org/Vol.10/March-2017/5.pdf fix_url=https://web.archive.org/web/20180721074940/http://www.veterinaryworld.org/Vol.10/March-2017/5.pdf + bad replacement URL: partial_ts=2017 original=https://www.ann-geophys.net/35/189/2017/angeo-35-189-2017.pdf fix_url=https://web.archive.org/web/20180625214916/https://www.ann-geophys.net/35/189/2017/angeo-35-189-2017.pdf + [...] + + # 9.96M 12:57:06 [ 213 /s] + + Counter({'total': 1272301, 'update': 1268466, 'skip-bad-wayback-timestamp': 2808, 'skip': 1026, 'skip-status': 981, 'skip-bad-replacement': 45, 'skip-bad-wayback': 1, 'insert': 0, 'exists': 0}) + Counter({'total': 1242814, 'update': 1239042, 'skip-bad-wayback-timestamp': 2734, 'skip': 1036, 'skip-status': 974, 'skip-bad-replacement': 62, 'skip-bad-wayback': 2, 'insert': 0, 'exists': 0}) + Counter({'total': 1264351, 'update': 1260695, 'skip-bad-wayback-timestamp': 2626, 'skip': 1030, 'skip-status': 977, 'skip-bad-replacement': 53, 'insert': 0, 'exists': 0}) + Counter({'total': 1244480, 'update': 1240779, 'skip-bad-wayback-timestamp': 2680, 'skip': 1020, 'skip-status': 962, 'skip-bad-replacement': 58, 'skip-bad-wayback': 1, 'insert': 0, 'exists': 0}) + Counter({'total': 1222678, 'update': 1219022, 'skip-bad-wayback-timestamp': 2698, 'skip': 956, 'skip-status': 892, 'skip-bad-replacement': 64, 'skip-bad-wayback': 2, 'insert': 0, 'exists': 0}) + Counter({'total': 1225078, 'update': 1221459, 'skip-bad-wayback-timestamp': 2597, 'skip': 1020, 'skip-status': 964, 'skip-bad-replacement': 56, 'skip-bad-wayback': 2, 'insert': 0, 'exists': 0}) + Counter({'total': 1283843, 'update': 1280014, 'skip-bad-wayback-timestamp': 2670, 'skip': 1059, 'skip-status': 997, 'skip-revision-changed': 99, 'skip-bad-replacement': 62, 'skip-bad-wayback': 1, 'insert': 0, 'exists': 0}) + Counter({'total': 1203309, 'update': 1199782, 'skip-bad-wayback-timestamp': 2556, 'skip': 971, 'skip-status': 923, 'skip-bad-replacement': 48, 'insert': 0, 'exists': 0}) + +On the order of 99.7% were updated/fixed, over 9.5 million file entities, taking almost 13 hours. diff --git a/extra/bulk_edits/2021-11-24_file_meta.md b/extra/bulk_edits/2021-11-24_file_meta.md new file mode 100644 index 00000000..1ec1698b --- /dev/null +++ b/extra/bulk_edits/2021-11-24_file_meta.md @@ -0,0 +1,41 @@ + +Another partial batch of pure `file_meta` updates to file entities. These came +from re-attempting ingest by URL of existing file entities. + +Not all ran as expected, partially because of GROBID issues, and partially +because we had alternate captures for the same URLs. + +Still, about half the attempts worked, so we are going to update a fraction of +the ~520k outstanding file entities with partial metadata (eg, missing sha256). + +See cleanups `file_meta` document for prep and QA testing notes. + + +## Production Commands + + git log | head -n1 + commit 75bde4ad3970e8e63b04009cfd16ed4b9a924ce7 + + export export FATCAT_AUTH_API_TOKEN=[...] # sandcrawler-bot + +Start with a small sample: + + 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': 100, 'skip-existing-complete': 45, 'update': 43, 'skip-no-match': 12, 'skip': 0, 'insert': 0, 'exists': 0}) + +Then run in parallel with full batch: + + cat /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': 41846, 'update': 19737, 'skip-existing-complete': 18788, 'skip-no-match': 3321, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 41522, 'update': 19678, 'skip-existing-complete': 18607, 'skip-no-match': 3237, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 41537, 'update': 20517, 'skip-existing-complete': 17895, 'skip-no-match': 3125, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 41529, 'update': 19684, 'skip-existing-complete': 18501, 'skip-no-match': 3344, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 41530, 'update': 19595, 'skip-existing-complete': 18637, 'skip-no-match': 3298, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 41542, 'update': 21359, 'skip-existing-complete': 17033, 'skip-no-match': 3150, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 41534, 'update': 19758, 'skip-existing-complete': 18516, 'skip-no-match': 3260, 'skip': 0, 'insert': 0, 'exists': 0}) + # Counter({'total': 41537, 'update': 20507, 'skip-existing-complete': 15543, 'skip-no-match': 5487, 'skip': 0, 'insert': 0, 'exists': 0}) + +Import ran pretty fast! Updated about 160k file entities. More like 1/3 than +1/2 of the 520k that were missing SHA-256. diff --git a/extra/bulk_edits/2021-11-24_file_sha1_dedupe.md b/extra/bulk_edits/2021-11-24_file_sha1_dedupe.md new file mode 100644 index 00000000..012bcf62 --- /dev/null +++ b/extra/bulk_edits/2021-11-24_file_sha1_dedupe.md @@ -0,0 +1,35 @@ + +See notes and scripts about `file_sha1_dedupe` cleanup for prep details. + +## Prod Run + +Run as `cleanup-bot`: + + export FATCAT_AUTH_API_TOKEN=[...] + + git log | head -n1 + # commit 5bc5eeed5e3ba54c2129c4233b881291c5fa7449 + +First do a sample in dry-run mode: + + 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 - + # Counter({'updated-entities': 59, 'lines': 25, 'merged': 25, 'skip': 0, 'updated-total': 0}) + +Gah, the dry-run mode still creates (empty) editgroups: + + https://fatcat.wiki/editgroup/iqzjg3vxu5elvotknmmjln3gv4 + https://fatcat.wiki/editgroup/2mxsl7lxo5dezem42whnr7zxxe + +Actually run (merge) the sample: + + 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({'updated-entities': 59, 'lines': 25, 'merged': 25, 'skip': 0, 'updated-total': 0}) + + +Run the full batch: + + cat /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': 6197, 'lines': 2039, 'merged': 2014, 'skip': 25, 'skip-not-active-entity': 25, 'updated-total': 0}) diff --git a/extra/bulk_edits/CHANGELOG.md b/extra/bulk_edits/CHANGELOG.md new file mode 100644 index 00000000..6156721c --- /dev/null +++ b/extra/bulk_edits/CHANGELOG.md @@ -0,0 +1,131 @@ + +# Fatcat Production Import CHANGELOG + +This file tracks major content (metadata) imports to the Fatcat production +database (at https://fatcat.wiki). It complements the code CHANGELOG file. + +In general, changes that impact more than 50k entities will get logged here; +this file should probably get merged into the guide at some point. + +This file should not turn in to a TODO list! + + +## 2021-11 + +Ran a series of cleanups. See background and prep notes in `notes/cleanups/` +and specific final commands in this directory. Quick summary: + +- more than 9.5 million file entities had truncated timestamps wayback URLs, + and were fixed with the full timestamps. there are still a small fraction + (0.5%) which were identified but not corrected in this first pass +- over 140k release entities with non-lowercase DOIs were updated with + lowercase DOI. all DOIs in current release entities now lowercase (at least, + no ASCII uppercase characters found) +- over 220k file entities with incorrect release relation, due to an + import-time code bug, were fixed. a couple hundred questionable cases remain, + but are all mismatched due to DOI slash/double-slash issues and will not be + fixed in an automated way. +- de-uplicated a few thousand file entities, on the basis of SHA-1 hash +- updated file metadata for around 160k file entities (a couple hundred + thousand remain with partial metadata) + + +## 2021-06 + +Created new containers via chocula pipeline. Did not update any existing +chocula entities. + +Ran DOAJ import manually, yielding almost 130k new release entities. + +Ran dblp import manually, resulting in about 17k new release entities, as well +as 108 new containers. Note that 146k releases were not inserted due to +`skip-dblp-container-missing` and 203k due to `exists-fuzzy`. + +## 2020-12 + +Updated ORCIDs from 2020 dump. About 2.4 million new `creator` entities. + +Imported DOAJ article metadata from a 2020-11 dump. Crawled and imported +several hundred thousand file entities matched by DOAJ identifier. Updated +journal metadata using chocula took (before the release ingest). Filtered out +fuzzy-matching papers before importing. + +Imported dblp from a 2020 snapshot, both containers (primarily for conferences +lacking an ISSN) and release entities (primarily conference papers). Filtered +out fuzzy-matching papers before importing. + +## 2020-03 + +Started harvesting both Arxiv and Pubmed metadata daily and importing to +fatcat. Did backfill imports for both sources. + +JALC DOI registry update from 2019 dump. + +## 2020-01 + +Imported around 2,500 new containers (journals, by ISSN-L) from chocula +analysis script. + +Imported DOIs from Datacite (around 16 million, plus or minus a couple +million). + +Imported new release entities from 2020 Pubmed/MEDLINE baseline. This import +included only new Pubmed works cataloged in 2019 (up until December or so). +Only a few hundred thousand new release entities. + +Daily "ingest" (crawling) pipeline running. + +## 2019-12 + +Started continuous harvesting Datacite DOI metadata; first date harvested was +`2019-12-13`. No importer running yet. + +Imported about 3.3m new ORCID identifiers from 2019 bulk dump (after converting +from XML to JSON): <https://archive.org/details/orcid-dump-2019> + +Inserted about 154k new arxiv release entities. Still no automatic daily +harvesting. + +"Save Paper Now" importer running. This bot only *submits* editgroups for +review, doesn't auto-accept them. + +## 2019-11 + +Daily ingest of fulltext for OA releases now enabled. New file entities created +and merged automatically. + +## 2019-10 + +Inserted 1.45m new release entities from Crossref which had been missed during +a previous gap in continuous metadata harvesting. + +Updated 304,308 file entities to remove broken +"https://web.archive.org/web/None/*" URLs. + +## 2019-09 + +Created and updated metadata for tens of thousands of containers, using +"chocula" pipeline. + +## 2019-08 + +Merged/fixed roughly 100 container entities with invalid ISSN-L numbers (eg, +invalid ISSN checksum). + +## 2019-04 + +Imported files (matched to releases by DOI) from Semantic Scholar +(`DIRECT-OA-CRAWL-2019` crawl). + +Imported files (matched to releases by DOI) from pre-1923/pre-1909 items uploaded +by a user to archive.org. + +Imported files (matched to releases by DOI) from CORE.ac.uk +(`DIRECT-OA-CRAWL-2019` crawl). + +Imported files (matched to releases by DOI) from the public web (including many +repositories) from the `UNPAYWALL` 2018 crawl. + +## 2019-02 + +Bootstrapped! |