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Diffstat (limited to 'notes/bulk_edits/2020_datacite.md')
| -rw-r--r-- | notes/bulk_edits/2020_datacite.md | 152 |
1 files changed, 0 insertions, 152 deletions
diff --git a/notes/bulk_edits/2020_datacite.md b/notes/bulk_edits/2020_datacite.md deleted file mode 100644 index 05d09517..00000000 --- a/notes/bulk_edits/2020_datacite.md +++ /dev/null @@ -1,152 +0,0 @@ - - -## 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 |