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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.
* 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
* 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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* do not normalize "en dash" in DOIMartin Czygan2020-01-171-2/+5
| | | | | | | | | 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 Newbold2020-01-151-3/+12
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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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* datacite: add entry to license slug mapMartin Czygan2020-01-091-0/+1
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* datacite: ignore known unknown values in resourceType*Martin Czygan2020-01-091-2/+2
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* datacite: abstracts may be strings or list of stringsMartin Czygan2020-01-091-2/+15
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* datacite: improve license_slug handlingMartin Czygan2020-01-091-60/+101
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* datacite: add 'Unknown' to blacklistMartin Czygan2020-01-091-1/+5
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* datacite: get rid of schemaVersionMartin Czygan2020-01-091-3/+0
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* Merge branch 'martin-datacite-import'Martin Czygan2020-01-082-0/+1024
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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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| * datacite: factor out contributor handlingMartin Czygan2020-01-081-80/+103
| | | | | | | | | | | | | | Use values from: * attributes.creators[] * attributes.contributors[]
| * datacite: catch type mismatch in language detectionMartin Czygan2020-01-081-3/+2
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| * datacite: name extra.month, extra.release_monthMartin Czygan2020-01-081-1/+3
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| * datacite: mark additional files as stubMartin Czygan2020-01-081-0/+4
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| * datacite: CCDC are entries, mostlyMartin Czygan2020-01-081-0/+4
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| * datacite: use more specific release_type, if possibleMartin Czygan2020-01-081-0/+6
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| * datacite: ignore certain namesMartin Czygan2020-01-081-0/+6
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| * datacite: over 3% records have the same title: stubMartin Czygan2020-01-081-0/+7
| | | | | | | | | | | | | | | | | | | | The GBIF (https://www.gbif.org/) deposits most records under the titles: * 599243 GBIF Occurrence Download * 41176 Occurrence Download Mark them as "stub" for the moment (https://guide.fatcat.wiki/entity_release.html#release_type-vocabulary).
| * datacite: fill a few more release_type gapsMartin Czygan2020-01-081-17/+18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * citeproc: http://docs.citationstyles.org/en/stable/specification.html#appendix-iii-types * resourceTypeGeneral: https://schema.datacite.org/meta/kernel-4.0/doc/DataCite-MetadataKernel_v4.0.pdf#page=32 * resourceType: uncontrolled, over 170000 distinct values, frequent: null, Dataset, JournalArticle, PGRFA Material, Journal Article, Dataset/UNITE Species Hypothesis, ... General frequency: * "attributes.types": 18210075, * "attributes.types.ris": 18058890, * "attributes.types.bibtex": 18058888, * "attributes.types.citeproc": 18058890, * "attributes.types.schemaOrg": 18058929, * "attributes.types.resourceType": 12737988, * "attributes.types.resourceTypeGeneral": 16576139,
| * datacite: adding datacite-specific extra metadataMartin Czygan2020-01-071-0/+28
| | | | | | | | | | | | | | | | | | | | | | | | | | * attributes.metadataVersion * attributes.schemaVersion * attributes.version (source dependent values, follows suggestions in https://schema.datacite.org/meta/kernel-4.3/doc/DataCite-MetadataKernel_v4.3.pdf#page=26, but values vary) Furthermore: * attributes.types.resourceTypeGeneral * attributes.types.resourceType
| * datacite: apply pylint suggestionsMartin Czygan2020-01-071-8/+10
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| * datacite: fix typosMartin Czygan2020-01-071-1/+1
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| * datacite: set release_stage to published by defaultMartin Czygan2020-01-061-4/+5
| | | | | | | | | | | | Set to `None` only if there is no publisher yet. Docs: https://support.datacite.org/docs/doi-states
| * datacite: month field should be top-levelMartin Czygan2020-01-061-2/+2
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