summaryrefslogtreecommitdiffstats
path: root/python/fatcat_tools
Commit message (Collapse)AuthorAgeFilesLines
* Merge branch 'bnewbold-cleanups-nov2021' into 'master'bnewbold2021-11-114-0/+748
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| |
| * cleanups: add more state=active checksBryan Newbold2021-11-092-0/+8
| |
| * update link source filters in file/release bugfixBryan Newbold2021-11-091-2/+8
| |
| * initial file/release bugfix cleanup worker and notesBryan Newbold2021-11-091-0/+231
| |
| * updates to lowercase DOI cleanupBryan Newbold2021-11-091-7/+15
| |
| * lowercase DOI lint and check entity statusBryan Newbold2021-11-091-4/+5
| |
| * more iteration on short wayback timestamp cleanupBryan Newbold2021-11-091-1/+1
| |
| * cleanups: tweaks to wayback CDX cleanup scriptsBryan Newbold2021-11-091-5/+13
| |
| * cleanups: initial lowercase DOI cleanup scriptBryan Newbold2021-11-091-0/+145
| |
| * wayback short ts: another regression test, and some small fmt/tweaksBryan Newbold2021-11-091-3/+38
| |
| * wayback cleanup: actually update entityBryan Newbold2021-11-091-2/+4
| |
| * imports: generic file cleanup removes exact duplicate URLsBryan Newbold2021-11-091-0/+9
| |
| * wayback short ts: add regression test for dupe URLsBryan Newbold2021-11-091-0/+44
| |
| * short wayback ts: initial cleanup script implementationBryan Newbold2021-11-091-0/+251
| |
* | 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.
* cleanups: create a separate JsonLinePusher for cleanup workers (distinct ↵Bryan Newbold2021-11-032-2/+19
| | | | base class)
* datacite importer: remove unused 'year_only' variableBryan Newbold2021-11-031-2/+3
|
* pubmed harvester: remove unused variablesBryan Newbold2021-11-031-2/+2
|
* pubmed harvester: explicit assertions to mark unreachable code pathsBryan Newbold2021-11-031-0/+2
|
* typing: add assertions to fatcat_tool code to make type assumptions explicitBryan Newbold2021-11-033-0/+3
|
* 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
|
* 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
|
* 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 Newbold2021-11-039-69/+129
| | | | | | 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 Newbold2021-11-028-50/+86
| | | | | | | | | 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.
* re-fix some lint issues after big 'fmt'Bryan Newbold2021-11-022-4/+5
|
* fmt (black): fatcat_tools/Bryan Newbold2021-11-0243-3194/+4020
|
* python: isort everythingBryan Newbold2021-11-0232-71/+116
|
* arabesque import 'hit' field is 1/0, not true/falseBryan Newbold2021-11-021-2/+2
|
* lint: simple, safe inline lint fixesBryan Newbold2021-11-0218-83/+82
| | | | '==' vs 'is'; 'not a in b' vs 'a not in b'; etc
* lint/fmt: remove all 'import *'Bryan Newbold2021-11-025-21/+41
|
* entity transforms: add basic type annotationsBryan Newbold2021-11-021-7/+19
|
* ftfy 'fix_entities' argument has been renamedBryan Newbold2021-11-021-4/+4
|
* hacks to work around new pylint false positivesBryan Newbold2021-11-021-2/+3
|
* cleanup imports after fatcat_tools.transforms changeBryan Newbold2021-11-021-5/+8
|
* re-fmt all the fatcat_tools __init__ files for readabilityBryan Newbold2021-11-025-30/+62
|
* remove 'import *' from fatcat_tools (for transforms)Bryan Newbold2021-11-021-2/+2
|
* small python tweaks for annotations, importsBryan Newbold2021-11-023-3/+7
|
* try some type annotationsBryan Newbold2021-11-024-70/+79
|
* reviewer: add annotations required by mypyBryan Newbold2021-11-021-2/+3
|
* fix missing variable in fileset ingestBryan Newbold2021-11-021-2/+1
|
* Merge branch 'bnewbold-import-fileset'Bryan Newbold2021-11-025-4/+350
|\
| * WIP: more fileset ingestBryan Newbold2021-10-181-13/+21
| |
| * WIP: rel fixesBryan Newbold2021-10-141-6/+6
| |
| * fileset ingest small tweaksBryan Newbold2021-10-141-21/+36
| |
generated by cgit v1.2.3 (git 2.39.1) at 2024-12-14 20:41:37 +0000