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| * remove cdl_dash_dat and wayback_static importersBryan Newbold2021-11-104-596/+0
| | | | | | | | | | | | | | | | Cleaning out dead code. These importers were used to create demonstration fileset and webcapture entities early in development. They have been replaced by the fileset and webcapture ingest importers.
| * datacite import: store less subject metadataBryan Newbold2021-11-101-1/+7
| | | | | | | | | | | | | | | | Many of these 'subject' objects have the equivalent of several lines of text, with complex URLs that don't compress well. I think it is fine we have included these thus far instead of parsing more deeply, but going forward I don't think this nested 'extra' metadata is worth the database space.
| * importers: use clean_doi() in many more (all?) importersBryan Newbold2021-11-096-12/+29
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| * clean_doi: stop mutating double-slash DOIs, except for 10.1037 prefixBryan Newbold2021-11-091-1/+2
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| * remove deprecated extid sqlite3 lookup table feature from importersBryan Newbold2021-11-0910-203/+10
| | | | | | | | | | | | | | | | This was used during initial bulk imports, but is no longer used and could create serious metadata problems if used accidentially. In retrospect, it also made metadata provenance less transparent, and may have done more harm than good overall.
* | Merge branch 'bnewbold-cleanups-nov2021' into 'master'bnewbold2021-11-115-1/+749
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fatcat metadata cleanups/fixups, November 2021 Three cleanups implemented in this branch: - update non-lowercase DOIs on releases (couple hundred thousand entities) - fix incorrectly imported file/release pairs, on the file entity side (~250k entities) - expand truncated wayback URL timestamps in file entities (up to 10 million entities) Instead of proposals, there are documents for each cleanup in `notes/cleanups/`. Have done spot testing of tens of thousands of entities each in QA, and confident about running in production. Plan is to run updates in the order above. DOI and bugfix updates will go fairly fast; the wayback timestamp updates will go slower, and result in large re-indexing load both in fatcat and scholar, because both release and work entities will get triggered for update when file entities are updated.
| * | file/release bugfix: handle files with multiple editsBryan Newbold2021-11-091-6/+6
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| * | cleanups: add more state=active checksBryan Newbold2021-11-092-0/+8
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| * | update link source filters in file/release bugfixBryan Newbold2021-11-091-2/+8
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| * | initial file/release bugfix cleanup worker and notesBryan Newbold2021-11-091-0/+231
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| * | updates to lowercase DOI cleanupBryan Newbold2021-11-091-7/+15
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| * | lowercase DOI lint and check entity statusBryan Newbold2021-11-091-4/+5
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| * | more iteration on short wayback timestamp cleanupBryan Newbold2021-11-091-1/+1
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| * | lint: minor import tweakBryan Newbold2021-11-091-1/+1
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| * | cleanups: tweaks to wayback CDX cleanup scriptsBryan Newbold2021-11-091-5/+13
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| * | cleanups: initial lowercase DOI cleanup scriptBryan Newbold2021-11-091-0/+145
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| * | wayback short ts: another regression test, and some small fmt/tweaksBryan Newbold2021-11-091-3/+38
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| * | wayback cleanup: actually update entityBryan Newbold2021-11-091-2/+4
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| * | imports: generic file cleanup removes exact duplicate URLsBryan Newbold2021-11-091-0/+9
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| * | wayback short ts: add regression test for dupe URLsBryan Newbold2021-11-091-0/+44
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| * | short wayback ts: initial cleanup script implementationBryan Newbold2021-11-091-0/+251
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* / pubmed: allow updates if PMCID does not exist yetBryan Newbold2021-11-101-1/+6
|/ | | | | | | | | | | The intent of this change is to start updating Pubmed metadata records when a PMCID has been assigned, but that ext_id hasn't been recorded in fatcat yet. It is likely that this change will result in some additional duplicate PMCIDs in the catalog. But the principle is that the PMID is the primary pubmed identifier, and all records with a PMID should have the PMCID that pubmed indicates, even if there exists another incorrect record.
* python tests: verify array sort orderBryan Newbold2021-11-054-20/+18
| | | | | | | In a couple cases (eg, filesets), had made tests agnostic to sort order, because the sort order was not stable. In other cases, simply small cleanups and comment improvements.
* enable type annotation checking with flake8 by default ('make lint')Bryan Newbold2021-11-031-4/+2
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* cleanups: create a separate JsonLinePusher for cleanup workers (distinct ↵Bryan Newbold2021-11-033-4/+20
| | | | base class)
* facat_import.py: work around corner case in run_cdl_dash_dat()Bryan Newbold2021-11-031-1/+1
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* datacite importer: remove unused 'year_only' variableBryan Newbold2021-11-031-2/+3
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* web: work around remaining type annotation issuesBryan Newbold2021-11-032-11/+15
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* ignore type errors in cors.py (third party code)Bryan Newbold2021-11-031-2/+2
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* web: fix bytes/text warning loggingBryan Newbold2021-11-031-3/+3
| | | | Minor issue. Caught by type checking
* lint: remove unused importBryan Newbold2021-11-031-1/+0
| | | | This was caught by new linting, I think not caused by any recent changes
* web config: add helper for coercing env vars into booleansBryan Newbold2021-11-031-3/+32
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* web: add type annotationsBryan Newbold2021-11-0312-297/+347
| | | | | This commit does not include type fixes, only annotations. A small number of tuples were also converted to lists.
* introduce 'AnyResponse' type for Flask viewsBryan Newbold2021-11-032-0/+15
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* pubmed harvester: remove unused variablesBryan Newbold2021-11-031-2/+2
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* pubmed harvester: explicit assertions to mark unreachable code pathsBryan Newbold2021-11-031-0/+2
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* typing: add assertions to fatcat_tool code to make type assumptions explicitBryan Newbold2021-11-033-0/+3
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* typing: add annotations to remaining fatcat_tools codeBryan Newbold2021-11-039-122/+186
| | | | | Again, these are just annotations, no changes made to get type checks to pass
* datacite: add comment about potential date parsing bugBryan Newbold2021-11-031-0/+1
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* datacite importer: dateparser.date.DateDataParser()Bryan Newbold2021-11-031-1/+1
| | | | Perhaps this was a change when upgrading 'dateparser'?
* more involved type wrangling and fixes for importersBryan Newbold2021-11-033-12/+14
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* typing: relatively simple type check fixesBryan Newbold2021-11-0314-87/+82
| | | | | | | These mostly add new variable names so that existing variables aren't overwritten with a new type; delay coercing '{}' or '[]' to 'None' until the last minute; adding is-not-None checks to conditional clauses; and similar small changes.
* typing: initial annotations on importersBryan Newbold2021-11-0322-274/+443
| | | | | This commit just adds the type annotations, doesn't do fixes to code to make type checking pass.
* typing: first batch of python bulk type annotationsBryan Newbold2021-11-0321-139/+200
| | | | | | While these changes are more delicate than simple lint changes, this specific batch of edits and annotations was *relatively* simple, and resulted in few code changes other than function signature additions.
* importers: remove unused __main__ routineBryan Newbold2021-11-034-19/+0
| | | | | | These perhaps were used in initial develoment or testing? fatcat_import.py is the correct way to do these imports, even for testing/development.
* lint: resolve existing mypy type errorsBryan Newbold2021-11-0212-81/+125
| | | | | | | | | Adds annotations and re-workes dataflow to satisfy existing mypy issues, without adding any additional type annotations to, eg, function signatures. There will probably be many more type errors when annotations are all added.
* web: annotate 'app' as 'Any', and document whyBryan Newbold2021-11-021-1/+5
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* flake8 config: update ignore list after big fmtBryan Newbold2021-11-021-3/+4
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* re-fix some lint issues after big 'fmt'Bryan Newbold2021-11-022-4/+5
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* fmt (black): fatcat_tools/Bryan Newbold2021-11-0243-3194/+4020
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