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* small python lint fixes (no behavior change)Bryan Newbold2021-05-251-1/+1
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* ingest: add per-container ingest type overridesBryan Newbold2021-05-211-1/+17
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* transforms: fix 'display_ame' typoBryan Newbold2021-04-191-2/+2
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* prefer contrib.creator.display_name over contrib.raw_nameBryan Newbold2021-04-122-4/+7
| | | | | | | | These will be getting updates from ORCID and are usually more complete and more correct for display, attribution, and search purposes. Might need to tweak fuzzycat code to handle multiple names at the verification stage.
* ES schema updates: doc_index_ts as a str, not datetimeBryan Newbold2021-04-061-4/+4
| | | | | The schema is a timestamp, but python needs to serialize as JSON, and doesn't do datetime automatically.
* container search schema: preservation stats, new fieldsBryan Newbold2021-04-061-2/+18
| | | | Includes transform code updates and partial test coverage.
* release ES: add discipline fieldBryan Newbold2021-04-061-0/+2
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* ES schemas: add doc_index_ts to all mappingsBryan Newbold2021-04-061-0/+4
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* elasticsearch: simple new dblp and doaj fieldsBryan Newbold2021-01-201-0/+4
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* bug fix: is_preserved should always be boolBryan Newbold2020-12-171-2/+2
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* fix indentationBryan Newbold2020-12-161-2/+2
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* have release elasticsearch transform count webcaptures and filesets towards ↵Bryan Newbold2020-12-161-26/+57
| | | | | | | | | | | | | preservation These are simple/partial changes to have webcaptures and filesets show up in 'preservation', 'in_ia', and 'in_web' ES schema flags. A longer-term TODO is to update the ES schema to have more granular analytic flags. Also includes a small generalization refactor for URL object parsing into preservation status, shared across file+fileset+webcapture entity types (all have similar URL objects with url+rel fields).
* small release_to_elasticsearch refactorsBryan Newbold2020-12-161-7/+12
| | | | | | | These should have almost no change in behavior, but improve code quality. The one behavior change is counting ftp URLs as "in_web"
* refactor release_to_elasticsearch transformBryan Newbold2020-12-161-131/+148
| | | | | | | | | | | | This method was huge an monolithic. This commit splits out the content and container specific sections into helper functions to make it more managable. This involved refactoring to make many flags ("is_*" and "in_*") part of the output dict through the entire code path, allowing simple update() calls on the dict. Noting that in the future should refactor to use a type-annotated class for the elasticsearch output object. Perhaps something auto-generated from the ES schema itself (JSON files).
* if a release has DOAJ article id, count as OABryan Newbold2020-11-191-0/+3
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* ingest tool: support for setting ingest typeBryan Newbold2020-11-061-6/+6
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* elastic transform: more preservation keepersBryan Newbold2020-10-081-1/+2
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* 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"
* basic toml transform helperBryan Newbold2020-07-302-4/+20
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* 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.
* lint (flake8) tool python filesBryan Newbold2020-07-014-18/+10
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* ES schema: add best_url to file schemaBryan Newbold2020-06-041-0/+12
| | | | | | | | | This will increase index size (URLs are often long in our corpus, and we have many file entities), but seems worth it. Initially added `ia_url` as a second field, guaranteed to always be an *.archive.org URL, but `best_url` defaults to that anyways so didn't seem worthwhile.
* improve citeproc/CSL web interfaceBryan Newbold2020-03-251-6/+12
| | | | | | | | | | | | | | This tries to show the citeproc (bibtext, MLA, CSL-JSON) options for more releases, and not show the links when they would break. The primary motivation here is to work around two exceptions being thrown in prod every day (according to sentry): KeyError: 'role' ValueError: CLS requries some surname (family name) I'm guessing these are mostly coming from crawlers following the citeproc links on release landing pages.
* Merge branch 'bnewbold-elastic-v03b'Bryan Newbold2020-02-262-46/+198
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| * improve is_oa flag accuracyBryan Newbold2020-02-261-8/+4
| | | | | | | | | | | | Particularly, the ezb=green match seems mostly incorrect. Note that pmcid being assigned could still be in an embargo window?
| * ES container last tweaksBryan Newbold2020-02-261-0/+3
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| * ES release: last minor tweaksBryan Newbold2020-02-261-2/+2
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| * ES files: don't remove archive.org domains/hostsBryan Newbold2020-02-071-5/+0
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| * ES releases: host/domain fixesBryan Newbold2020-01-311-2/+2
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| * fix release es transform missing 'issue'Bryan Newbold2020-01-301-0/+1
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| * add upper-case work-around from kibana map joinBryan Newbold2020-01-301-0/+1
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| * tweak file ES archive.org domain trackingBryan Newbold2020-01-301-0/+6
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| * implement host+domain parsing for file ES transformBryan Newbold2020-01-301-9/+5
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| * fix ES file schema plural field namesBryan Newbold2020-01-291-4/+3
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| * elastic schema fixesBryan Newbold2020-01-291-0/+5
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| * add country to v03b release schemaBryan Newbold2020-01-291-0/+2
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| * actually implement changelog transformBryan Newbold2020-01-291-17/+45
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| * fix some transform bugs, add some testsBryan Newbold2020-01-291-6/+8
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| * ES release schema updatesBryan Newbold2020-01-291-5/+76
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| * container ES schema changesBryan Newbold2020-01-291-16/+18
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| * first implementation of ES file schemaBryan Newbold2020-01-292-1/+46
| | | | | | | | | | Includes a trivial test and transform, but not any workers or doc updates.
* | default to PMC ingest URLs over DOIBryan Newbold2020-02-041-4/+4
|/ | | | | | | For cases where there might be both PMC and DOI urls, do the europmc.org PMC ones over DOI option. May want to turn this into a config or command-line option in the future.
* remove 'oa_only' feature from ingest transformBryan Newbold2020-01-281-14/+1
| | | | Refactoring to move this filter elsewhere
* transform ingests via pmc/pmcid, not pubmed/pmidBryan Newbold2019-12-241-4/+4
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* update ingest request schemaBryan Newbold2019-12-131-5/+22
| | | | | This is mostly changing ingest_type from 'file' to 'pdf', and adding 'link_source'/'link_source_id', plus some small cleanups.
* tweaks to ingest-file transformBryan Newbold2019-12-121-13/+7
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* project -> ingest_request_sourceBryan Newbold2019-11-151-2/+2
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* fix release.pmcid typoBryan Newbold2019-11-151-2/+2
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* more ingest importer comments and countsBryan Newbold2019-11-151-1/+1
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