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* pipenv: update pytest to 5.x; remove langcodesBryan Newbold2020-01-032-108/+85
| | | | | | | | | | pytest has been pinned to the 4.x series to work around a test import package mangling problem with citeproc_styles. Now that pytest.ini explicitly lists test files, this seems to no longer be a problem and pytest can be updated to the most recent version. Also re-locked Pipfile.lock with updated dependencies (only minor changes).
* pytest: explicitly indicate all in-scope test filesBryan Newbold2020-01-031-3/+1
| | | | | | | | | | | The purpose of this change is to test errors when pytest tries to recursively update assertion statements in all dependent packages. The reason pytest does this is to add pretty printing, which is nice, but probably shouldn't be done in all dependency libraries. This fixes test problems with both CSL (citeproc_styles) and dateparser (when actually imported in code, which currently on master does not happen).
* orcid: skip non-person ORCID recordsBryan Newbold2019-12-261-0/+4
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* datacite: fix harvest testMartin Czygan2019-12-271-1/+1
| | | | | | Produced messages should match: jq '.data|length' tests/files/datacite_api.json
* datacite: add simple test and fixture for datacite api interactionMartin Czygan2019-12-272-0/+46
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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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* add regression test for medlinedate -> year parsingBryan Newbold2019-12-232-0/+102
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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.
* datacite release links and metadata expansionBryan Newbold2019-12-202-9/+13
| | | | | | | Small ergonomic changes for datacite releases: - add a link to live/current datacite metadata (like we do for Crossref) - expand "extra" metadata fields under 'datacite' dict in metadata view
* spn: incluce link_source/link_source_id in ingest requestBryan Newbold2019-12-201-0/+2
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* pipenv: update depsBryan Newbold2019-12-172-11/+55
| | | | | | | | loginpass patches got accepted upstream a while back, so don't need to pin to a git version ipython 7.10 seems to have problems installing, so restricting to earlier 6.x versions
* pipenv: restrict pytest<5.0.0Bryan Newbold2019-12-172-5/+13
| | | | | | | | | | | | | | | | | | | | | | | | | This prevents a test exception that presents like: tests/transform_csl.py:46: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ fatcat_tools/transforms/csl.py:204: in citeproc_csl style_path = get_style_filepath(style) .venv/lib/python3.5/site-packages/citeproc_styles/__init__.py:74: in get_style_filepath if resource_exists(__name__, independent_style): .venv/lib/python3.5/site-packages/pkg_resources/__init__.py:1134: in resource_exists return get_provider(package_or_requirement).has_resource(resource_name) .venv/lib/python3.5/site-packages/pkg_resources/__init__.py:1404: in has_resource return self._has(self._fn(self.module_path, resource_name)) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pkg_resources.NullProvider object at 0x7f4f38c0bb00> path = '/home/bnewbold/code/fatcat/python/.venv/lib/python3.5/site-packages/citeproc_styles/styles/bibtex.csl' def _has(self, path): raise NotImplementedError( > "Can't perform this operation for unregistered loader type" ) E NotImplementedError: Can't perform this operation for unregistered loader type
* pipenv: update Pipfile and Pipfile.lockBryan Newbold2019-12-172-286/+318
| | | | | | This is still manually tweaked. I believe i've bifurcated the source of the CSL/citeproc_style import error to upgrade of the 'pytest' module. This commit upgrades all packages except pytest.
* pipfile: add langcodes and dateparser dependenciesBryan Newbold2019-12-172-1/+44
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* 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.
* | fix spn kafka topic env varBryan Newbold2019-12-131-1/+1
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* | update ingest request schemaBryan Newbold2019-12-135-16/+44
| | | | | | | | | | 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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* | initial 'Save Paper Now' web formBryan Newbold2019-12-127-2/+228
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* | more auth token vars in example.envBryan Newbold2019-12-121-0/+6
| | | | | | | | As a form of documentation
* | savepapernow result importerBryan Newbold2019-12-123-4/+89
| | | | | | | | 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.
* Merge branch 'bnewbold-ingest-oa-container' into 'master'bnewbold2019-12-126-3/+181
|\ | | | | | | | | container-ingest tool See merge request webgroup/fatcat!8
| * container_issnl, not issnl, for ES release queryBryan Newbold2019-12-121-1/+1
| | | | | | | | Caught by Martin in review; Thanks!
| * improve argparse usageBryan Newbold2019-12-111-6/+4
| | | | | | | | | | | | | | | | | | | | --fatcat-api-url is clearer than --host-url remove unimplemented --debug (copy/paste from webface argparse) use formater which will display 'default' parameters with --help Thanks to Martin for pointing out the later, which i've always wanted!
| * simplify ES scroll deletion using param()Bryan Newbold2019-12-111-29/+29
| | | | | | | | | | | | | | | | | | | | | | This gets rid of some mess error handling code by properly configuring the elasticsearch client to just not clean up scroll iterators when accessing the public (prod or qa) search interfaces. Leaving the scroll state around isn't ideal, so we still delete them if possible (eg, connecting directly to elasticsearch). Thanks to Martin for pointing out this solution in review.
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