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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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* entity updater: handle doi=None case betterBryan Newbold2020-08-141-1/+1
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* entity updater: es['publisher_type'] not always setBryan Newbold2020-08-141-1/+1
| | | | This is a small bugfix for a production issue.
* Merge branch 'bnewbold-ingest-improvements' into 'master'Martin Czygan2020-08-132-33/+114
|\ | | | | | | | | ingest behavior changes; some datacite metadata tweaks See merge request webgroup/fatcat!78
| * entity update: change big5 ingest behaviorBryan Newbold2020-08-111-9/+15
| | | | | | | | | | | | | | | | | | In addition to changing the OA default, this was the main intended behavior change in this group of commits: want to ingest fewer attempts that we *expect* to fail, but default to ingest/crawl attempt if we are uncertain. This is because there is a long tail of journals that register DOIs and are defacto OA (fulltext is available), but we don't have metadata indicating them as such.
| * entity update: default to ingest non-OA worksBryan Newbold2020-08-111-9/+10
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| * entity update: skip ingest of figshare+zenodo 'group' DOIsBryan Newbold2020-08-111-0/+15
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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
| * update crawl blocklist for SPNv2 requests which mostly failBryan Newbold2020-08-101-2/+10
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* | harvest: datacite API yields HTTP 200 with broken JSONMartin Czygan2020-08-101-1/+8
|/ | | | As a first step: log response body for debugging.
* release ES transform tweaksBryan Newbold2020-08-071-3/+5
| | | | | | | | pass-through publisher_type from container extra metadata (ES field already existed; this is from newer chocula metadata) count arxiv and PMCID papers which haven't been crawled (by IA) as "dark", not "bright"
* 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'
* basic toml transform helperBryan Newbold2020-07-302-4/+20
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* Merge branch 'bnewbold-more-lint-fixes' into 'master'Martin Czygan2020-07-246-25/+18
|\ | | | | | | | | more lint fixes See merge request webgroup/fatcat!69
| * 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.
* | simplify in_kbart check statementBryan Newbold2020-07-231-1/+1
| | | | | | | | Thanks @martin
* | make in_kbart transform inclusive of last yearBryan Newbold2020-07-231-0/+9
|/ | | | | | | | | | | | | | | | | Frequently when looking at preservation coverage of journals, the current year shows as "un-preserved" when in fact there is robust KBART (keepers, eg CLOCKSS/Portico) coverage. This is partially because we don't update containers with KBART year spans very frequently (which is on us), and partially because KBART reports are often a bit out of day (eg, doesn't show coverage for the current year. For that matter, they probably take a few months to update the previous year as well, but that is a larger time span to fudge over. This patch means we will count Portico/LOCKSS/etc coverage for "last year" to count as coverage of publications dated "this year". Note that for this to be effective/correct, it is assumed that we will update containers with coverage year spans at least once a year, and that we will re-index all releases at least once a year.
* 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 Czygan2020-07-1033-133/+51
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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
* | | Merge branch 'martin-datacite-bugfix-sentry-44035' into 'master'bnewbold2020-07-111-0/+4
|\ \ \ | |_|/ |/| | | | | | | | datacite: mitigate sentry #44035 See merge request webgroup/fatcat!66
| * | 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.
* | | Merge branch 'martin-arxiv-fix-http-503' into 'master'bnewbold2020-07-101-1/+1
|\ \ \ | |/ / |/| | | | | | | | arxiv: address 503, "Retry after specified interval" error See merge request webgroup/fatcat!64
| * | arxiv: do retry five times of HTTP 503Martin Czygan2020-07-101-1/+1
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* | | datacite: fix attribute errorMartin Czygan2020-07-071-1/+1
|/ / | | | | | | refs: #44035
* | lint (flake8) tool python filesBryan Newbold2020-07-0133-130/+46
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* | reviewer: fix bugs in common code found by mypyBryan Newbold2020-07-011-2/+3
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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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* disallow a specific unicode character from DOIsBryan Newbold2020-06-261-0/+6
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* ES schema: add best_url to file schemaBryan Newbold2020-06-041-0/+12
| | | | | | | | | This will increase index size (URLs are often long in our corpus, and we have many file entities), but seems worth it. Initially added `ia_url` as a second field, guaranteed to always be an *.archive.org URL, but `best_url` defaults to that anyways so didn't seem worthwhile.
* harvest: fail on HTTP 400Martin Czygan2020-05-291-4/+0
| | | | | | | | | In the past harvest of datacite resulted in occasional HTTP 400. Meanwhile, various API bugs have been fixed (most recently: https://github.com/datacite/lupo/pull/537, https://github.com/datacite/datacite/issues/1038). Downside of ignoring this error was that state lives in kafka, which has limited support for deletion of arbitrary messages from a topic.
* Merge branch 'bnewbold-ingest-stage' into 'master'Martin Czygan2020-05-281-0/+5
|\ | | | | | | | | verify release_stage in ingest importer See merge request webgroup/fatcat!52
| * ingest importer: check that stage is consistent with releaseBryan Newbold2020-05-261-0/+5
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* | rename HarvestState.next() to HarvestState.next_span()Bryan Newbold2020-05-264-5/+5
|/ | | | | | | | | "span" short for "timespan" to harvest; there may be a better name to use. Motivation for this is to work around a pylint erorr that .next() was not callable. This might be a bug with pylint, but .next() is also a very generic name.
* HACK: skip pylint errors on lines that seem to be fineBryan Newbold2020-05-223-3/+3
| | | | | It seems to be an inadvertantly ugraded version of pylint saying that these lines are not-callable.
* Merge remote-tracking branch 'github/master'Bryan Newbold2020-05-221-2/+2
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| * Indentity is not the same this as equality in PythonChristian Clauss2020-05-141-2/+2
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