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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
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