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* 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.
* ingest: add 'extid' and 'query' modes; filters; refactorBryan Newbold2020-02-041-38/+147
| | | | | | This is a large refactor of the ingest script. It adds a number of filtering options (for all modes), and new modes for free-form queries or limiting to specific external identifiers.
* 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 Czygan2020-01-312-1/+7
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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 Czygan2020-01-304-21/+153
| | | | | | | | | | | | | 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.
* 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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| * datacite: reformat test cases and use jq . --sort-keysMartin Czygan2020-01-0854-2299/+2301
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| * datacite: factor out contributor handlingMartin Czygan2020-01-086-82/+210
| | | | | | | | | | | | | | Use values from: * attributes.creators[] * attributes.contributors[]
| * datacite: catch type mismatch in language detectionMartin Czygan2020-01-081-3/+2
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| * datacite: adjust tests for release_monthMartin Czygan2020-01-0812-12/+12
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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 Czygan2020-01-084-1/+77
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| * datacite: CCDC are entries, mostlyMartin Czygan2020-01-082-1/+5
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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 Czygan2020-01-0731-1468/+1598
| | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Czygan2020-01-072-2/+2
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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
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