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