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| -rw-r--r-- | notes/bulk_edits/2020_datacite.md | 152 |
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diff --git a/notes/bulk_edits/2020_datacite.md b/notes/bulk_edits/2020_datacite.md new file mode 100644 index 00000000..005841ae --- /dev/null +++ b/notes/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 noticable? + +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 |