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authorBryan Newbold <bnewbold@robocracy.org>2020-01-19 09:53:18 -0800
committerBryan Newbold <bnewbold@robocracy.org>2020-01-19 09:58:18 -0800
commit0bdd96ced29b86cb15133b27038301bc9eecef30 (patch)
tree66798a7bfc28abaac9cddd44486fce4551eba499
parent0742d0904166192ed48cd83e604a4d95246dfa47 (diff)
downloadfatcat-0bdd96ced29b86cb15133b27038301bc9eecef30.tar.gz
fatcat-0bdd96ced29b86cb15133b27038301bc9eecef30.zip
bulk edit notes for datacite (QA)
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+
+
+## 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