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* fixes for newer ref indexBryan Newbold2021-07-232-50/+11
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* web: inbound/outbound refs as links (temporarily); change URL namesBryan Newbold2021-07-233-3/+7
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* web: initial implementation of fuzzy citation parsing and matching toolBryan Newbold2021-07-233-0/+173
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* references: refactor to point to access_options transform; comment out CSL ↵Bryan Newbold2021-07-231-57/+8
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* partial access options transform for releasesBryan Newbold2021-07-231-0/+58
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* web: template macro to display release entry summaryBryan Newbold2021-07-231-0/+52
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* first iteration of basic citation inbound/outbound viewsBryan Newbold2021-07-233-1/+146
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* initial inbound/outbound reference query helpersBryan Newbold2021-07-231-0/+450
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* pubmed: update docsMartin Czygan2021-07-171-2/+3
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* pubmed: do not fail when accessing missing fileMartin Czygan2021-07-171-2/+8
| | | | | | | after a sync gap (e.g. 06/07 2021) harvester wanted to fetch a file, that was not on the server (any more) - do not fail in this case we'll need to backfill missing records via full data dump
* pubmed: reconnect on errorMartin Czygan2021-07-161-4/+30
| | | | | | | | | ftp retrieval would run but fail with EOFError on /pubmed/updatefiles/pubmed21n1328_stats.html - not able to find the root cause; using a fresh client, the exact same file would work just fine. So when we retry, we reconnect on failure. Refs: sentry #91102.
* web: fix flask/werkzeug encoding for mediawiki oauthBryan Newbold2021-07-131-1/+4
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* web: fix missing ext_ids default for deleted entity viewBryan Newbold2021-07-131-1/+1
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* web: fix 'file' entity edit form linksBryan Newbold2021-07-021-1/+1
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* web: missing trailing parensBryan Newbold2021-07-021-1/+1
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* web: PMCID external link improvementBryan Newbold2021-07-022-2/+2
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* Merge branch 'bnewbold-more-doi-lower' into 'master'Martin Czygan2021-07-023-3/+8
|\ | | | | | | | | more consistent and defensive lower-casing of DOIs See merge request webgroup/fatcat!109
| * more consistent and defensive lower-casing of DOIsBryan Newbold2021-06-233-3/+8
| | | | | | | | | | | | | | After noticing more upper/lower ambiguity in production. In particular, we have some old ingest requests in sandcrawler DB, which get re-submitted/re-tried, which have capitalized DOIs in the link source id field.
* | tests: small citeproc style changes (to match Pipfile.lock update)Bryan Newbold2021-06-232-3/+4
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* | pipenv: regenerate lock fileBryan Newbold2021-06-231-26/+68
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* | pipenv: add pydantic; add surt; narrow dynaconfBryan Newbold2021-06-231-1/+3
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* datacite: more careful title string access; fixes sentry #88350Martin Czygan2021-06-114-2/+97
| | | | | Caused by a partial "title entry without title" coming *first* (e.g. just holding, e.g. a language, like: {'lang': 'da'}
* clean_doi() should lower-case returned DOIBryan Newbold2021-06-071-1/+4
| | | | | | | | | | Code in a number of places (including Pubmed importer) assumed that this was already lower-casing DOIs, resulting in some broken metadata getting created. See also: https://github.com/internetarchive/fatcat/issues/83 This is just the first step of mitigation.
* web: fix DOAJ article links (remove trailing slash)Bryan Newbold2021-06-041-1/+1
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* dblp tests: skip redundant seek(0)Bryan Newbold2021-06-031-6/+1
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* ingest: swap ingest and file checks, to result in clearer stats/counts of ↵Bryan Newbold2021-06-031-2/+2
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* ingest: don't accept mag and s2 URLsBryan Newbold2021-06-031-4/+4
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* bump fuzzycat dependency to 0.1.21Bryan Newbold2021-06-022-20/+18
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* web: fix spacing for doaj/dblp identifiers in SERPBryan Newbold2021-05-311-1/+1
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* ingest: don't 'track_total_hits' for ES 7.x count()Bryan Newbold2021-05-311-1/+1
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* web: bugfix dblp vs. doaj display logicBryan Newbold2021-05-311-1/+1
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* update fuzzycat to 0.1.20Bryan Newbold2021-05-312-31/+94
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* makefile: add pylint -E invocation to 'make lint', to match CIBryan Newbold2021-05-251-0/+1
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* skip pylint on 'assigning-non-slot' warnings in Flask 2.0Bryan Newbold2021-05-251-2/+2
| | | | | | | | | | | | | | The 'permanent' field is still valid to set to a boolean in Flask 2.0; not sure why pylint is unhappy in CI (causing test failures). Don't see any problem running test suite locally. Flask API docs: https://flask.palletsprojects.com/en/2.0.x/api/?highlight=permanent#flask.session.permanent And code (recent master branch): https://github.com/pallets/flask/blob/4240ace59710d86c478111affd4ad6fb4c8cad9e/src/flask/sessions.py#L20
* changelog worker: fix file/fileset typo, caught by lintBryan Newbold2021-05-251-1/+1
| | | | | This would have been resulting in some releases not getting re-indexed into search.
* small python lint fixes (no behavior change)Bryan Newbold2021-05-255-6/+4
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* bump Flask to 2.x; other deps upgraded automaticallyBryan Newbold2021-05-212-152/+167
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* ingest: add per-container ingest type overridesBryan Newbold2021-05-212-1/+23
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* fix arabesque sqlite3 examples to have 14-digit timestampsBryan Newbold2021-05-211-0/+0
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* arabesque importer: ensure full 14-digit timestampsBryan Newbold2021-05-211-1/+3
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* Andrew W. Mellon FoundationBryan Newbold2021-05-182-3/+3
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* Merge branch 'bnewbold-pipenv-cleanup' into 'master'bnewbold2021-04-232-327/+277
|\ | | | | | | | | pipenv cleanup See merge request webgroup/fatcat!104
| * pipenv: re-lock projectBryan Newbold2021-04-191-301/+253
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| * pipenv: constrain most package versions to at least majorBryan Newbold2021-04-191-24/+24
| | | | | | | | | | | | | | | | | | Don't have a complete policy with this change, just locking things down a bit more so small package additions and updates don't end up upgrading some small dependency to a major new backwards-incompatible version. Also, correct bs4 -> beautifulsoup4 (bs4 is the import name, not the package name)
| * pipenv: remove unused pg-view and pykafka librariesBryan Newbold2021-04-191-2/+0
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* | web: fix edit form style guide linksBryan Newbold2021-04-202-4/+4
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* transforms: fix 'display_ame' typoBryan Newbold2021-04-191-2/+2
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* web: expand release creators in more situationsBryan Newbold2021-04-192-2/+2
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* fix public API linksBryan Newbold2021-04-151-2/+2
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* fix 'colected' typosBryan Newbold2021-04-131-1/+1
| | | | Thanks for the catch martin
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