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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?
* fix fatcat_transform state filtersBryan Newbold2020-02-261-4/+4
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* bulk ES transform: skip non-active entitiesBryan Newbold2020-02-261-0/+8
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* 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 updates: fix tests to accept archive.org in host/domainBryan Newbold2020-02-141-2/+3
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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 Newbold2020-01-312-2/+5
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* pipenv: lock zipp version to work around python3.6 requirementBryan Newbold2020-01-302-7/+20
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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 Newbold2020-01-302-13/+8
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* pipenv: add tldextract (url parser) and update depsBryan Newbold2020-01-302-136/+159
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* fix ES file schema plural field namesBryan Newbold2020-01-292-5/+4
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* new biblio-only general searchBryan Newbold2020-01-291-2/+2
| | | | The other fields are now "copy_to" the merged biblio field.
* 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 Newbold2020-01-292-18/+68
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* fix some transform bugs, add some testsBryan Newbold2020-01-296-13/+48
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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 Newbold2020-01-293-3/+69
| | | | | Includes a trivial test and transform, but not any workers or doc updates.
* 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.
* increase kafka-pixy timeout to 25 secondsBryan Newbold2020-01-281-1/+1
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* 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 Newbold2020-01-282-15/+1
| | | | Refactoring to move this filter elsewhere
* refactor fatcat_import kafka group namesBryan Newbold2020-01-211-13/+54
| | | | | | | | | | | | | My current understanding is that consumer group names should be one-to-one with topic names. I previously though offsets were stored on a {topic, group} key, but they seem to be mixed and having too many workers in the same group is bad. In particular, we don't want cross-talk or load between QA and prod. All these topics are caught up in prod, so deploying this change and restarting workers should be safe. This commit does not update the elasticsearch or entity updates workers.
* fix trivial typo in file importerBryan Newbold2020-01-201-1/+1
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* normal: DOI corner-case from pubmed importBryan Newbold2020-01-191-0/+9
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* Merge branch 'martin-fix-container-search' into 'master'Martin Czygan2020-01-182-6/+6
|\ | | | | | | | | pagination: use correct endpoint in navigation See merge request webgroup/fatcat!19
| * pagination: use correct endpoint in navigationMartin Czygan2020-01-182-6/+6
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* | fix trivial one-character typo in fatcat_import.pyBryan Newbold2020-01-171-1/+1
| | | | | | | | Should have run tests before pushing!
* | actually control pubmed updates with a flagBryan Newbold2020-01-171-0/+4
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* | do not normalize "en dash" in DOIMartin Czygan2020-01-172-3/+6
|/ | | | | | | | | Technically, [...] DOI names may incorporate any printable characters from the Universal Character Set (UCS-2), of ISO/IEC 10646, which is the character set defined by Unicode (https://www.doi.org/doi_handbook/2_Numbering.html#2.5.1). For mostly QA reasons, we currently treat a DOI with an "en dash" as invalid.
* ingest: improve tests, support old ingest resultsBryan Newbold2020-01-154-4/+30
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* update ingest worker for schema tweaksBryan Newbold2020-01-151-8/+15
| | | | | | Should be backwards compatible with old ingest results. Fixed a bug with glutton ident detection.
* ingest: allow more sources to auto-importBryan Newbold2020-01-151-1/+2
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* datacite: skip records without a doiMartin Czygan2020-01-131-0/+4
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* add missing sentry/raven tagsBryan Newbold2020-01-103-2/+19
| | | | | | Good to have exceptions tracked and stored even for commands run from the command line. But in particular the importer runs as a kafka worker and should be tracking excpetions.
* datacite: add entry to license slug mapMartin Czygan2020-01-092-0/+2
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* datacite: ignore known unknown values in resourceType*Martin Czygan2020-01-094-3/+97
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* datacite: abstracts may be strings or list of stringsMartin Czygan2020-01-096-3/+202
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* datacite: improve license_slug handlingMartin Czygan2020-01-094-62/+134
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* datacite: add 'Unknown' to blacklistMartin Czygan2020-01-092-8/+6
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* datacite: get rid of schemaVersionMartin Czygan2020-01-0918-35/+14
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* update depsMartin Czygan2020-01-081-86/+69
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* Merge branch 'martin-datacite-import'Martin Czygan2020-01-0864-5/+5736
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Pipfile.lock is broken. * martin-datacite-import: (68 commits) datacite: pass in doi into factored out method datacite: reformat test cases and use jq . --sort-keys datacite: factor out contributor handling datacite: catch type mismatch in language detection datacite: adjust tests for release_month datacite: name extra.month, extra.release_month datacite: mark additional files as stub datacite: CCDC are entries, mostly datacite: use more specific release_type, if possible datacite: ignore certain names datacite: over 3% records have the same title: stub datacite: fill a few more release_type gaps datacite: adding datacite-specific extra metadata datacite: apply pylint suggestions datacite: fix typos datacite: set release_stage to published by default datacite: month field should be top-level datacite: include month in extra datacite: indicate mismatched file in test datacite: clean abstracts, use unknown value tokens ...
| * datacite: pass in doi into factored out methodMartin Czygan2020-01-081-2/+3
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