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* more python normalizers, and move from importer commonBryan Newbold2020-11-192-154/+326
| | | | | | | | | | | | 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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* ingest tool: support for setting ingest typeBryan Newbold2020-11-061-6/+6
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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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* normalizer: filter out a specific non-ASCII character in DOIBryan Newbold2020-11-041-1/+3
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* entity updates: don't ingest JSTOR DOI prefixesBryan Newbold2020-10-231-0/+2
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* entity updater: new work update feed (ident and changelog metadata only)Bryan Newbold2020-10-161-2/+24
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* chocula importer: small tweaks to update behaviorBryan Newbold2020-10-081-8/+6
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* elastic transform: more preservation keepersBryan Newbold2020-10-081-1/+2
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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.
* ingest: default to crawl protocols.io DOIsBryan Newbold2020-09-101-0/+2
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* 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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* 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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