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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.
* | datacite: prevent noneMartin Czygan2020-01-311-1/+1
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* | datacite: name shall not be NoneMartin Czygan2020-01-311-1/+1
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* | datacite: add exception for https://www.micropublication.org/Martin Czygan2020-01-311-0/+5
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* | datacite: do not skip records w/o dateMartin Czygan2020-01-311-2/+1
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* | datacite: improve docstringMartin Czygan2020-01-311-4/+4
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* | datacite: improve date handling and minor tweakMartin Czygan2020-01-301-19/+42
|/ | | | | | | | | | | | | Records from https://www.micropublication.org/ did not have a date in FC, although raw data contained date strings - they were not using the finer-grained "attributes.date" but "attributes.published" and/or "attributes.publicationYear". Support for those fields has been added, including a test case. During this test (#30) a processing gap for names became clear (author may have "given_name" and "surname", but no "name"). This bug has been fixed, too.
* fix KafkaError worker reporting for partition errorsBryan Newbold2020-01-293-3/+3
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* additional DOI prefix filtersBryan Newbold2020-01-281-0/+8
| | | | From martin, thanks.
* apply ingest request filtering in entity workerBryan Newbold2020-01-281-3/+34
| | | | | | | `ingest_oa_only` behavior, and other filters, now handled in the entity update worker, instead of in the transform function. Also add a DOI prefix blocklist feature.
* remove 'oa_only' feature from ingest transformBryan Newbold2020-01-281-14/+1
| | | | Refactoring to move this filter elsewhere
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