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* improve datacite field mapping and importMartin Czygan2019-12-281-41/+139
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Current version succeeded to import a random sample of 100000 records (0.5%) from datacite. The --debug (write JSON to stdout) and --insert-log-file (log batch before committing to db) flags are temporary added to help debugging. Add few unit tests. Some edge cases: a) Existing keys without value requires a slightly awkward: ``` titles = attributes.get('titles', []) or [] ``` b) There can be 0, 1, or more (first one wins) titles. c) Date handling is probably not ideal. Datacite has a potentiall fine grained list of dates. The test case (tests/files/datacite_sample.jsonl) refers to https://ssl.fao.org/glis/doi/10.18730/8DYM9, which has date (main descriptor) 1986. The datacite record contains: 2017 (publicationYear, probably the year of record creation with reference system), 1978-06-03 (collected, e.g. experimental sample), 1986 ("Accepted"). The online version of the resource knows even one more date (2019-06-05 10:14:43 by WIEWS update).
* datacite: add missing mappings and notesMartin Czygan2019-12-281-266/+175
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* datacite: basic field mappingsMartin Czygan2019-12-281-41/+181
| | | | | | | | | | Currently using two external libraries: * dateparser * langcodes Note: This commit includes lots of wip docs and field stat in comment, which should be removed.
* datacite: importer skeletonMartin Czygan2019-12-282-0/+459
| | | | | | * contributors, title, date, publisher, container, license Field and value analysis via https://github.com/miku/indigo.
* orcid: skip non-person ORCID recordsBryan Newbold2019-12-261-0/+4
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* datacite: extend range search queryMartin Czygan2019-12-271-1/+1
| | | | | The bracket syntax is inclusive. See also: https://www.elastic.co/guide/en/elasticsearch/reference/7.5/query-dsl-query-string-query.html#_ranges
* avoid usage of short linksMartin Czygan2019-12-271-2/+2
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* Datacite API v2 throws 400, we cannot recover from, currently.Martin Czygan2019-12-271-0/+4
| | | | | | | | | | As a first iteration, just mark the daily batch complete and continue. The occasional HTTP 400 issue has been reported as https://github.com/datacite/datacite/issues/897. A possible improvement would be to shrink the window, so losses will be smaller.
* datacite: update documentation, add links to issuesMartin Czygan2019-12-271-10/+5
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* datacite: use v2 of the API (flaky)Martin Czygan2019-12-271-5/+28
| | | | | | | | | Update parameter update for datacite API v2. Works fine, but there are occasional HTTP 400 responses when using the cursor API (daily updates can exceed the 10000 record limit for search queries). The HTTP 400 issue is not solved yet, but reported to datacite as https://github.com/datacite/datacite/issues/897.
* transform ingests via pmc/pmcid, not pubmed/pmidBryan Newbold2019-12-241-4/+4
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* allow arabesque backfill ingests for some source typesBryan Newbold2019-12-241-0/+5
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* make chocula URL updates more conservativeBryan Newbold2019-12-241-5/+5
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* pubmed: if doing update, also do subtitle schema updateBryan Newbold2019-12-231-1/+9
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* doi parsing fixesBryan Newbold2019-12-231-0/+7
| | | | | | | | | | Replace emdash with regular dash. Replace double slash after partner ID with single slash. This conversion seems to be done by crossref automatically on lookup. I tried several examples, using doi.org resolver and Crossref API lookup. Note that there are a number of fatcat entities with '//' in the DOI.
* pubmed: improve warning and stderr formattingBryan Newbold2019-12-231-5/+6
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* pubmed: use standard identifier cleanersBryan Newbold2019-12-231-17/+14
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* pubmed: remove unused extid mapping codeBryan Newbold2019-12-231-29/+0
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* pubmed: do reference lookups by defaultBryan Newbold2019-12-231-1/+1
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* normalizers: clean_pmid(), and handle nulls in all other cleanersBryan Newbold2019-12-231-0/+31
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* pubmed: null doi parsing checkBryan Newbold2019-12-231-1/+1
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* add basic MedlineDate year parsingBryan Newbold2019-12-231-0/+11
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* fix spn/ingest importer duplication checkBryan Newbold2019-12-221-6/+8
| | | | | | Check was happing after the `return True` by mistake, allowing duplicates in SPN editgroups, and potentially in ingest request editgroups as well.
* write diagnostic messages to stderrMartin Czygan2019-12-161-2/+2
| | | | | During debugging, it can be helpful to keep stdout (e.g. processing results) and dignostic messages separate.
* Merge branch 'martin-importers-common-doc-fix' into 'master'Martin Czygan2019-12-141-13/+10
|\ | | | | | | | | Update EntityImporter docstring. See merge request webgroup/fatcat!9
| * complete parse_record docstringMartin Czygan2019-12-141-0/+6
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| * Update EntityImporter docstring.Martin Czygan2019-12-131-13/+4
| | | | | | | | I believe the required method is `parse_record`, not `parse`.
* | add ingest import file collision protectionBryan Newbold2019-12-131-0/+6
| | | | | | | | | | | | | | | | The common case is the same URL being submitted repeatedly during testing. This is only within-editgroup, and per importer (eg, won't work across spn importer "submitted" editgroups), but is better than nothing.
* | update ingest request schemaBryan Newbold2019-12-133-8/+30
| | | | | | | | | | This is mostly changing ingest_type from 'file' to 'pdf', and adding 'link_source'/'link_source_id', plus some small cleanups.
* | remove default mimetype from ingest-file importerBryan Newbold2019-12-131-2/+1
| | | | | | | | We really should just use file_meta result or nothing.
* | revert accidentally commited test timingBryan Newbold2019-12-131-2/+2
| | | | | | | | Also fix a spurious typo.
* | ensure importer description arg isn't clobberedBryan Newbold2019-12-123-5/+5
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* | tweaks to ingest-file transformBryan Newbold2019-12-121-13/+7
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* | savepapernow result importerBryan Newbold2019-12-122-4/+65
| | | | | | | | Based on ingest-file-results importer
* | flush importer editgroups every few minutesBryan Newbold2019-12-121-5/+20
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* | EntityImporter: submit (not accept) modeBryan Newbold2019-12-121-2/+14
|/ | | | | For use with bots that don't have admin privileges, or where human follow-up review is desired.
* factor out some basic kafka helpersBryan Newbold2019-12-102-0/+23
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* add another ingest request source to whitelistBryan Newbold2019-12-101-2/+5
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* refactor kafka producer in crossref harvesterBryan Newbold2019-12-061-21/+26
| | | | | | | | producer creation/configuration should be happening in __init__() time, not 'daily' call. This specific refactor motivated by mocking out the producer in unit tests.
* tweaks to file ingest importerBryan Newbold2019-12-031-3/+4
| | | | | - allow overriding source filter whitelist (common case for CLI use) - fix editgroup description env variable pass-through
* crossref is_update isn't what I thoughtBryan Newbold2019-12-031-6/+2
| | | | | | | | I thought this would filter for metadata updates to an existing DOI, but actually "updates" are a type of DOI (eg, a retraction). TODO: handle 'updates' field. Should both do a lookup and set work_ident appropriately, and store in crossref-specific metadata.
* re-order ingest want() for better statsBryan Newbold2019-11-151-7/+10
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* project -> ingest_request_sourceBryan Newbold2019-11-153-9/+9
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* fix release.pmcid typoBryan Newbold2019-11-151-2/+2
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* ingest importer fixesBryan Newbold2019-11-151-3/+4
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* more ingest importer comments and countsBryan Newbold2019-11-152-2/+29
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* crude support for 'sandcrawler' kafka topicsBryan Newbold2019-11-151-2/+3
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* ingest file result importerBryan Newbold2019-11-152-2/+135
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* add ingest request feature to entity_updates workerBryan Newbold2019-11-151-4/+20
| | | | | | | | | | | | | Initially was going to create a new worker to consume from the release update channel, but couldn't get the edit context ("is this a new release, or update to an existing") from that context. Currently there is a flag in source code to control whether we only do OA releases or all releases. Starting with OA only to start slow, but should probably default to all, and make this a config flag. Should probably also have a config flag to control this entire feature. Tested locally in dev.
* add ingest request transform (and test)Bryan Newbold2019-11-152-0/+67
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