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* remove isascii() work around definition in importers/datacite.pyBryan Newbold2020-07-231-7/+1
| | | | We are python3.7 now, so this isn't needed.
* simple lint (flake8) fixes over python codebaseBryan Newbold2020-07-231-7/+7
| | | | | | These should not have any behavior changes, though a number of exception catches are now more general, and there may be long-tail exceptions getting thrown in these statements.
* Merge branch 'martin-datacite-duplicated-author-gh-59' into 'master'bnewbold2020-07-111-6/+60
|\ | | | | | | | | datacite: address duplicated contributor issue See merge request webgroup/fatcat!65
| * datacite: resolve formatting issues in testsMartin Czygan2020-07-101-2/+1
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| * | datacite: there should be no index gapsMartin Czygan2020-07-101-2/+8
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| * | datacite: document contributor typesMartin Czygan2020-07-101-0/+25
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| * | wip: contrib, GH59Martin Czygan2020-07-101-16/+22
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| * | datacite: address duplicated contributor issueMartin Czygan2020-07-071-0/+16
| | | | | | | | | | | | | | | | | | | | | Use string comparison. * https://fatcat.wiki/release/spjysmrnsrgyzgq6ise5o44rlu/contribs * https://api.datacite.org/dois/10.25940/roper-31098406
* | | datacite: mitigate sentry #44035Martin Czygan2020-07-101-0/+4
| |/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | According to sentry, running `c.get('nameIdentifiers', []) or []` on a c with value: ``` {'affiliation': [], 'familyName': 'Guidon', 'givenName': 'Manuel', 'nameIdentifiers': {'nameIdentifier': 'https://orcid.org/0000-0003-3543-6683', 'nameIdentifierScheme': 'ORCID', 'schemeUri': 'https://orcid.org'}, 'nameType': 'Personal'} ``` results in a string, which I cannot reproduce. The document in question at: https://api.datacite.org/dois/10.26275/kuw1-fdls seems fine, too.
* | datacite: fix attribute errorMartin Czygan2020-07-071-1/+1
| | | | | | | | refs: #44035
* | lint (flake8) tool python filesBryan Newbold2020-07-011-2/+0
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* add new license mappingsBryan Newbold2020-06-301-0/+14
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* datacite: improve license mappingMartin Czygan2020-06-301-9/+15
| | | | via "missed potential license", refs #58
* datacite: hard cast possible date value to stringMartin Czygan2020-06-291-1/+1
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* datacite: fix type errorMartin Czygan2020-04-221-1/+3
| | | | | | | Up to now, we expected the description to be a string or list. Add handling for int as well. First appeared: Apr 22 19:58:39.
* datacite: fix a raw name constraint violationMartin Czygan2020-04-201-0/+8
| | | | | | | It was possible that contribs got added which had no raw name. One example would be a name consisting of whitespace only. This fix adds a final check for this case.
* Merge pull request #53 from EdwardBetts/spellingbnewbold2020-03-271-4/+4
|\ | | | | Correct spelling mistakes
| * Correct spelling mistakesEdward Betts2020-03-271-4/+4
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* | datacite: nameIdentifier corner caseBryan Newbold2020-03-261-1/+2
| | | | | | | | | | | | | | | | | | Works around a bug in production: AttributeError: 'NoneType' object has no attribute 'replace' (datacite.py:724) NOTE: there are no tests for this code path
* | datacite: add year sanity restrictionsbnewbold2020-03-231-0/+7
|/ | | | | | | | | Example of entities with bogus years: https://fatcat.wiki/release/search?q=doi_registrar%3Adatacite+year%3A%3E2100 We can do a clean-up task, but first need to prevent creation of new bad metadata.
* 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.
* 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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* 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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* datacite: include month in extraMartin Czygan2020-01-061-0/+2
| | | | | > include release_month as a top-level extra field [...] to auto-populate the schema field from that
* datacite: clean abstracts, use unknown value tokensMartin Czygan2020-01-061-4/+26
| | | | | | | | Datacite defines placeholders for unknown values: * https://support.datacite.org/docs/schema-values-unknown-information-v43 Clean abstracts.
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