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* wrap up basic (locally testable) ingest refactorBryan Newbold2020-01-093-182/+267
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* cli: allow multiple ingest single typesBryan Newbold2020-01-091-3/+4
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* example.env: more required varsBryan Newbold2020-01-091-2/+7
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* basic elife+plos extraction testsBryan Newbold2020-01-093-0/+4842
| | | | | Ripped out some HTML, but these could have been minimized even further to keep repository from growing large.
* fix grobid test (ISO-8859-1 encoding)Bryan Newbold2020-01-091-6/+4
| | | | Also changes for wayback refactor
* fix grobid tests for new wayback refactorsBryan Newbold2020-01-093-15/+17
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* more wayback and SPN tests and fixesBryan Newbold2020-01-094-52/+220
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* pipenv: mock testing libraryBryan Newbold2020-01-092-309/+325
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* refactor CdxApiClient, add testsBryan Newbold2020-01-082-40/+240
| | | | | | - always use auth token and get full CDX rows - simplify to "fetch" (exact url/dt match) and "lookup_best" methods - all redirect stuff will be moved to a higher level
* refactor SavePaperNowClient and add testBryan Newbold2020-01-072-28/+314
| | | | | | - response as a namedtuple - "remote" errors (aka, SPN API was HTTP 200 but returned error) aren't an exception
* remove SPNv1 code pathsBryan Newbold2020-01-072-65/+25
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* TODO: check out python ratelimit libraryBryan Newbold2020-01-021-1/+1
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* handle grobid2json errors in calling code insteadBryan Newbold2020-01-021-1/+7
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* db: move duplicate row filtering into DB insert helpersBryan Newbold2020-01-022-15/+26
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* remove unused filter in grobid workerBryan Newbold2020-01-021-1/+0
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* fix dict typoBryan Newbold2020-01-021-1/+1
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* improvements to grobid persist workerBryan Newbold2020-01-021-13/+16
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* update persist worker invocation to use batchesBryan Newbold2020-01-021-15/+55
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* set mimetype when PUT to minioBryan Newbold2020-01-021-0/+4
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* fix DB import countingBryan Newbold2020-01-021-4/+5
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* include an example environment fileBryan Newbold2020-01-021-0/+2
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* teixml2json test update for skipping null JSON keysBryan Newbold2020-01-021-10/+1
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* fix small errors found by pylintBryan Newbold2020-01-022-1/+2
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* fix sandcrawler persist workersBryan Newbold2020-01-022-8/+37
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* filter ingest results to not have key conflicts within batchBryan Newbold2020-01-021-1/+16
| | | | | This handles a corner case with ON CONFLICT ... DO UPDATE where you can't do multiple such updates in the same batch transaction.
* db: fancy insert/update separation using postgres xmaxBryan Newbold2020-01-022-24/+45
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* add PersistGrobidDiskWorkerBryan Newbold2020-01-022-0/+60
| | | | To help with making dumps directly from Kafka (eg, for partner delivery)
* flush out minio helper, add to grobid persistBryan Newbold2020-01-023-24/+91
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* implement counts properly for persist workersBryan Newbold2020-01-021-15/+19
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* improve DB helpersBryan Newbold2020-01-021-26/+81
| | | | | - return insert/update row counts - implement ON CONFLICT ... DO UPDATE on some tables
* be more parsimonious with GROBID metadataBryan Newbold2020-01-022-3/+20
| | | | | Because these are getting persisted in database (as well as kafka), don't write out empty keys.
* start work on DB connector and minio clientBryan Newbold2020-01-022-0/+200
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* have JsonLinePusher continue on JSON decode errors (but count)Bryan Newbold2020-01-021-1/+5
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* start work on persist workers and toolBryan Newbold2020-01-023-5/+336
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* update TODOBryan Newbold2019-12-261-1/+7
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* basic arabesque2ingestrequest scriptBryan Newbold2019-12-241-0/+69
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* commit grobid_tool transform modeBryan Newbold2019-12-221-0/+27
| | | | Had some stale code on aitio with this change I forgot to commit. Oops!
* refactor: use print(..., file=sys.stderr)Bryan Newbold2019-12-185-32/+34
| | | | Should use logging soon, but this seems more idiomatic in the meanwhile.
* refactor: sort keys in JSON outputBryan Newbold2019-12-184-6/+7
| | | | This makes debugging by tailing Kafka topics a lot more readable
* refactor: improve argparse usageBryan Newbold2019-12-185-13/+27
| | | | | use ArgumentDefaultsHelpFormatter and add help messages to all sub-commands
* update ingest proposal source/link namingBryan Newbold2019-12-131-1/+1
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* fixes for large GROBID result skipBryan Newbold2019-12-021-2/+2
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* count empty blobs as 'failed' instead of crashingBryan Newbold2019-12-011-1/+2
| | | | Might be better to record an artificial kafka response instead?
* cleanup unused importBryan Newbold2019-12-011-1/+0
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* filter out very large GROBID XML bodiesBryan Newbold2019-12-011-0/+6
| | | | | | | | | | This is to prevent Kafka MSG_SIZE_TOO_LARGE publish errors. We should probably bump this in the future. Open problems: hand-coding this size number isn't good, need to update in two places. Shouldn't filter out for non-Kafka sinks. Might still exist a corner-case where JSON encoded XML is larger than XML character string, due to encoding (eg, for unicode characters).
* CI: make some jobs manualBryan Newbold2019-11-151-0/+2
| | | | | Scalding test is broken :( But we aren't even using that code much these days.
* handle wayback fetch redirect loop in ingest codeBryan Newbold2019-11-141-2/+5
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* bump kafka max poll interval for consumersBryan Newbold2019-11-141-2/+2
| | | | | The ingest worker keeps timing out at just over 5 minutes, so bump it just a bit.
* handle WaybackError during ingestBryan Newbold2019-11-141-0/+4
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* handle SPNv1 redirect loopBryan Newbold2019-11-141-0/+2
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