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* add 'lxml' mode for large XML file import, and multi-tagsBryan Newbold2020-12-171-15/+28
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* add dblp as an ingest source and identifierBryan Newbold2020-12-171-1/+2
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* ingest: allow doaj ingest responsesBryan Newbold2020-12-171-1/+2
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* update fuzzy helper to pass 'reason' through to import codeBryan Newbold2020-12-171-3/+3
| | | | | The motivation for this change is to enable passing the 'reason' through to edit extra metadata, in cases where we merge or cluster releases.
* add fuzzy match filtering to DOAJ importerBryan Newbold2020-12-161-2/+9
| | | | | | | | | | | In this default configuration, any entities with a fuzzy match (even "ambiguous") will be skipped at import time, to prevent creating duplicates. This is conservative towards not creating new/duplicate entities. In the future, as we get more confidence in fuzzy match/verification, we can start to ignore AMBIGUOUS, handle EXACT as same release, and merge STRONG (and WEAK?) matches under the same work entity.
* add fuzzy matching helper to importer base classBryan Newbold2020-12-161-2/+62
| | | | Using fuzzycat. Add basic test coverage.
* html ingest: small fixes to try_update() code pathBryan Newbold2020-12-151-5/+5
| | | | | Don't currently have test coverage for most try_update() code; run the inserts manually in testing.
* crossref+datacite: remove confusing early update bailBryan Newbold2020-11-202-4/+0
| | | | | Easy to miss that we skip updates *twice*, and with this early bailout were not updating counts correctly.
* doaj: fix update code path (getattr not __dict__)Bryan Newbold2020-11-201-4/+3
| | | | Also add missing code coverage for update path (disabled by default).
* DOAJ: handle empty identifier 'id' caseBryan Newbold2020-11-201-0/+2
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* tweak DOAJ importer class args and default for do_updatesBryan Newbold2020-11-191-2/+2
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* implement remainder of DOAJ article importerBryan Newbold2020-11-191-57/+125
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* more python normalizers, and move from importer commonBryan Newbold2020-11-191-154/+4
| | | | | | | | | | | | Moved several normalizer helpers out of fatcat_tools.importers.common to fatcat_tools.normal. Copied language name and country name parser helpers from chocula repository (built on existing pycountry helper library). Have not gone through and refactored other importers to point to these helpers yet; that should be a separate PR when this branch is merged. Current changes are backwards compatible via re-imports.
* initial implementation of DOAJ importerBryan Newbold2020-11-192-0/+290
| | | | Several things to finish implementing and polish.
* html ingest: actual xhtml mimetypeBryan Newbold2020-11-161-2/+2
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* html ingest: remaining implementationBryan Newbold2020-11-061-22/+19
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* ingest: progress on HTML ingestBryan Newbold2020-11-051-14/+30
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* ingest: initial 'web' worker implementationBryan Newbold2020-11-052-67/+259
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* refactor: white/black -> allow/blockBryan Newbold2020-11-051-4/+4
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* ingest: whitelist -> allowlistBryan Newbold2020-11-051-3/+3
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* ingest: basic checks for ingest_typeBryan Newbold2020-11-051-3/+29
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* chocula importer: small tweaks to update behaviorBryan Newbold2020-10-081-8/+6
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* address spammy datacite titlesMartin Czygan2020-09-231-0/+19
| | | | | | | | | seemingly from zenodo: * https://fatcat.wiki/release/rzcpjwukobd4pj36ipla22cnoi * https://doi.org/10.5281/zenodo.4041777 About 3400 records with "FULL MOVIE" in title, currently.
* datacite: handle case of empty-string versionBryan Newbold2020-09-101-1/+1
| | | | | Includes a tiny tweak to the datacite import sample file to test this code path.
* remove spurious print statementBryan Newbold2020-09-031-1/+0
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* generic file entity clean-ups as part of file_meta importerBryan Newbold2020-09-022-0/+50
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* fix comment typo (thanks martin)Bryan Newbold2020-08-271-1/+1
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* fixes and test coverage for file_meta importerBryan Newbold2020-08-211-5/+10
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* initial implementation of file_meta importerBryan Newbold2020-08-212-0/+71
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* datacite import: figshare-specific hacksBryan Newbold2020-08-111-3/+3
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* datacite import: refactor release_type detection into static methodBryan Newbold2020-08-111-14/+51
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* datacite import: refactor publisher-specific hacks into static methodBryan Newbold2020-08-111-15/+29
| | | | Also tweak title/publisher detection to use DOI prefixes
* chocula import update tweaksBryan Newbold2020-08-041-10/+14
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* more update keys and cases for chocula importerBryan Newbold2020-08-041-5/+11
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* fix key name mismatch in chocula importerBryan Newbold2020-08-041-1/+1
| | | | chocula 'export-fatcat' uses 'ident', not 'fatcat_ident'
* fix issnl typo in pubmedBryan Newbold2020-07-231-1/+1
| | | | | | | | | | Oh no! This bug may actually have had significant negative impact on metadata in fatcat, in terms of missing container_id associations with pubmed entities. There are about 500k release entities with a PMID but no container_id. Of those, 89k have at least a container_name. Unclear how many would have matched to ISSN-L and thus to a container.
* 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 Newbold2020-07-235-17/+16
| | | | | | 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 Czygan2020-07-1016-72/+28
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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 Newbold2020-07-0116-72/+27
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* add new license mappingsBryan Newbold2020-06-302-0/+27
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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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