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* | Merge branch 'martin-kafka-bs4-import' into 'master'Martin Czygan2020-03-105-22/+318
|\ \ | |/ |/| | | | | pubmed and arxiv harvest preparations See merge request webgroup/fatcat!28
| * common: use smaller batch size since XML parsing may be slowMartin Czygan2020-03-101-1/+1
| | | | | | | | | | | | | | | | Address kafka tradeoff between long and short time-outs. Shorter time-outs would facilitate > consumer group re-balances and other consumer group state changes [...] in a reasonable human time-frame.
| * pubmed: log to stderrMartin Czygan2020-03-101-1/+1
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| * pubmed: move mapping generation out of fetch_dateMartin Czygan2020-03-101-7/+8
| | | | | | | | | | * fetch_date will fail on missing mapping * adjust tests (test will require access to pubmed ftp)
| * harvest: fix imports from HarvestPubmedWorker cleanupMartin Czygan2020-03-101-2/+2
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| * pubmed: citations is a bit more preciseMartin Czygan2020-03-091-1/+1
| | | | | | | | | | > Each day, NLM produces update files that include new, revised and deleted citations. -- ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/README.txt
| * pubmed: we sync from FTPMartin Czygan2020-03-091-1/+1
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| * oaipmh: HarvestPubmedWorker obsoleted by PubmedFTPWorkerMartin Czygan2020-03-091-34/+0
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| * more pubmed adjustmentsMartin Czygan2020-02-222-70/+118
| | | | | | | | | | * regenerate map in continuous mode * add tests
| * pubmed ftp: fix urlMartin Czygan2020-02-191-4/+6
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| * pubmed ftp harvest and KafkaBs4XmlPusherMartin Czygan2020-02-194-1/+280
| | | | | | | | | | | | | | * add PubmedFTPWorker * utils are currently stored alongside pubmed (e.g. ftpretr, xmlstream) but may live elsewhere, as they are more generic * add KafkaBs4XmlPusher
* | Merge branch 'bnewbold-elastic-v03b'Bryan Newbold2020-02-262-46/+198
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| * | improve is_oa flag accuracyBryan Newbold2020-02-261-8/+4
| | | | | | | | | | | | | | | | | | Particularly, the ezb=green match seems mostly incorrect. Note that pmcid being assigned could still be in an embargo window?
| * | ES container last tweaksBryan Newbold2020-02-261-0/+3
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| * | ES release: last minor tweaksBryan Newbold2020-02-261-2/+2
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| * | ES files: don't remove archive.org domains/hostsBryan Newbold2020-02-071-5/+0
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| * | ES releases: host/domain fixesBryan Newbold2020-01-311-2/+2
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| * | fix release es transform missing 'issue'Bryan Newbold2020-01-301-0/+1
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| * | add upper-case work-around from kibana map joinBryan Newbold2020-01-301-0/+1
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| * | tweak file ES archive.org domain trackingBryan Newbold2020-01-301-0/+6
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| * | implement host+domain parsing for file ES transformBryan Newbold2020-01-301-9/+5
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| * | fix ES file schema plural field namesBryan Newbold2020-01-291-4/+3
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| * | elastic schema fixesBryan Newbold2020-01-291-0/+5
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| * | add country to v03b release schemaBryan Newbold2020-01-291-0/+2
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| * | actually implement changelog transformBryan Newbold2020-01-291-17/+45
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| * | fix some transform bugs, add some testsBryan Newbold2020-01-291-6/+8
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| * | ES release schema updatesBryan Newbold2020-01-291-5/+76
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| * | container ES schema changesBryan Newbold2020-01-291-16/+18
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| * | first implementation of ES file schemaBryan Newbold2020-01-292-1/+46
| | | | | | | | | | | | | | | Includes a trivial test and transform, but not any workers or doc updates.
* | | Merge branch 'bnewbold-more-ingest' into 'master'bnewbold2020-02-251-1/+37
|\ \ \ | | | | | | | | | | | | | | | | entity worker: ingest more Datacite releases; filter some out See merge request webgroup/fatcat!29
| * | | entity worker: ingest more releasesBryan Newbold2020-02-221-1/+37
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | If release is a dataset or image, don't do a pdf ingest request. If release is a datacite DOI, and release_type is a "document", crawl regardless of is_oa detection. This is mostly to crawl repositories (institutional or subject).
* | | | add some more domain/rel URL mappingsBryan Newbold2020-02-221-0/+9
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* | | Merge branch 'bnewbold-shadow-import'Bryan Newbold2020-02-192-0/+196
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| * | | remove arabesque short wayback URL hackBryan Newbold2020-02-141-6/+0
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| * | | improve shadow import file url cleanup pathBryan Newbold2020-02-131-2/+12
| | | | | | | | | | | | | | | | Should probably be refactored out in to shared cleanup code.
| * | | shadow import fixes from QA testingBryan Newbold2020-02-131-0/+6
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| * | | shadow import: more filtering of file_meta fieldsBryan Newbold2020-02-131-0/+10
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| * | | basic shadow importerBryan Newbold2020-02-132-0/+176
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* | | | always crawl researchgate DOIsBryan Newbold2020-02-181-0/+2
| | | | | | | | | | | | | | | | Now that ingest is fixed
* | | | ingest import: fix edit_extra pathBryan Newbold2020-02-181-1/+1
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* | | | ingest importer: edit_extra is a top-level keyBryan Newbold2020-02-181-1/+1
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* | | | ingest import: allow short version of corpus namesBryan Newbold2020-02-181-0/+3
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* | | | ingest importer: pass through link relBryan Newbold2020-02-181-1/+6
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* | | harvest: log state on startup and use stderr for diagnosticsMartin Czygan2020-02-143-17/+22
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* | add acceptlist override for biorxiv/medrxivBryan Newbold2020-02-101-2/+12
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* | check ingest_request_source existance for SPN as well as ingestBryan Newbold2020-02-061-0/+3
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* | additional trusted link sourcesBryan Newbold2020-02-061-0/+3
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* | add mag and s2 as trusted link sourcesBryan Newbold2020-02-061-1/+1
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* | ingest worker: handle missing ingest_request_sourceBryan Newbold2020-02-061-0/+3
| | | | | | | | | | Seeing a bunch of these due to re-ingests not including this field because of an earlier persist bug.
* | default to PMC ingest URLs over DOIBryan Newbold2020-02-041-4/+4
| | | | | | | | | | | | | | For cases where there might be both PMC and DOI urls, do the europmc.org PMC ones over DOI option. May want to turn this into a config or command-line option in the future.
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