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* | | | fatcat_ingest: as 'fatcat-ingest', not 'fatcat-ingest-container' | Bryan Newbold | 2020-02-14 | 1 | -1/+1 | |
| | | | | | | | | | | | | This tool is more generic now. | |||||
* | | | harvest: log state on startup and use stderr for diagnostics | Martin Czygan | 2020-02-14 | 3 | -17/+22 | |
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* | | add acceptlist override for biorxiv/medrxiv | Bryan Newbold | 2020-02-10 | 1 | -2/+12 | |
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* | | check ingest_request_source existance for SPN as well as ingest | Bryan Newbold | 2020-02-06 | 1 | -0/+3 | |
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* | | additional trusted link sources | Bryan Newbold | 2020-02-06 | 1 | -0/+3 | |
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* | | add mag and s2 as trusted link sources | Bryan Newbold | 2020-02-06 | 1 | -1/+1 | |
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* | | ingest worker: handle missing ingest_request_source | Bryan Newbold | 2020-02-06 | 1 | -0/+3 | |
| | | | | | | | | | | Seeing a bunch of these due to re-ingests not including this field because of an earlier persist bug. | |||||
* | | switch '!= None' to 'is not None' | Bryan Newbold | 2020-02-04 | 1 | -3/+3 | |
| | | | | | | | | As reminded in code review, thanks Martin. | |||||
* | | allow-non-oa is a top-level flag, not sub-command | Bryan Newbold | 2020-02-04 | 1 | -3/+0 | |
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* | | default to PMC ingest URLs over DOI | Bryan Newbold | 2020-02-04 | 1 | -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. | |||||
* | | ingest: add 'extid' and 'query' modes; filters; refactor | Bryan Newbold | 2020-02-04 | 1 | -38/+147 | |
| | | | | | | | | | | | | This is a large refactor of the ingest script. It adds a number of filtering options (for all modes), and new modes for free-form queries or limiting to specific external identifiers. | |||||
* | | datacite: prevent none | Martin Czygan | 2020-01-31 | 1 | -1/+1 | |
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* | | datacite: name shall not be None | Martin Czygan | 2020-01-31 | 1 | -1/+1 | |
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* | | datacite: add exception for https://www.micropublication.org/ | Martin Czygan | 2020-01-31 | 2 | -1/+7 | |
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* | | datacite: do not skip records w/o date | Martin Czygan | 2020-01-31 | 1 | -2/+1 | |
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* | | datacite: improve docstring | Martin Czygan | 2020-01-31 | 1 | -4/+4 | |
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* | | datacite: improve date handling and minor tweak | Martin Czygan | 2020-01-30 | 4 | -21/+153 | |
|/ | | | | | | | | | | | | | Records from https://www.micropublication.org/ did not have a date in FC, although raw data contained date strings - they were not using the finer-grained "attributes.date" but "attributes.published" and/or "attributes.publicationYear". Support for those fields has been added, including a test case. During this test (#30) a processing gap for names became clear (author may have "given_name" and "surname", but no "name"). This bug has been fixed, too. | |||||
* | fix KafkaError worker reporting for partition errors | Bryan Newbold | 2020-01-29 | 3 | -3/+3 | |
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* | additional DOI prefix filters | Bryan Newbold | 2020-01-28 | 1 | -0/+8 | |
| | | | | From martin, thanks. | |||||
* | increase kafka-pixy timeout to 25 seconds | Bryan Newbold | 2020-01-28 | 1 | -1/+1 | |
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* | apply ingest request filtering in entity worker | Bryan Newbold | 2020-01-28 | 1 | -3/+34 | |
| | | | | | | | `ingest_oa_only` behavior, and other filters, now handled in the entity update worker, instead of in the transform function. Also add a DOI prefix blocklist feature. | |||||
* | remove 'oa_only' feature from ingest transform | Bryan Newbold | 2020-01-28 | 2 | -15/+1 | |
| | | | | Refactoring to move this filter elsewhere | |||||
* | refactor fatcat_import kafka group names | Bryan Newbold | 2020-01-21 | 1 | -13/+54 | |
| | | | | | | | | | | | | | My current understanding is that consumer group names should be one-to-one with topic names. I previously though offsets were stored on a {topic, group} key, but they seem to be mixed and having too many workers in the same group is bad. In particular, we don't want cross-talk or load between QA and prod. All these topics are caught up in prod, so deploying this change and restarting workers should be safe. This commit does not update the elasticsearch or entity updates workers. | |||||
* | fix trivial typo in file importer | Bryan Newbold | 2020-01-20 | 1 | -1/+1 | |
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* | normal: DOI corner-case from pubmed import | Bryan Newbold | 2020-01-19 | 1 | -0/+9 | |
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* | Merge branch 'martin-fix-container-search' into 'master' | Martin Czygan | 2020-01-18 | 2 | -6/+6 | |
|\ | | | | | | | | | pagination: use correct endpoint in navigation See merge request webgroup/fatcat!19 | |||||
| * | pagination: use correct endpoint in navigation | Martin Czygan | 2020-01-18 | 2 | -6/+6 | |
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* | | fix trivial one-character typo in fatcat_import.py | Bryan Newbold | 2020-01-17 | 1 | -1/+1 | |
| | | | | | | | | Should have run tests before pushing! | |||||
* | | actually control pubmed updates with a flag | Bryan Newbold | 2020-01-17 | 1 | -0/+4 | |
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* | | do not normalize "en dash" in DOI | Martin Czygan | 2020-01-17 | 2 | -3/+6 | |
|/ | | | | | | | | | Technically, [...] DOI names may incorporate any printable characters from the Universal Character Set (UCS-2), of ISO/IEC 10646, which is the character set defined by Unicode (https://www.doi.org/doi_handbook/2_Numbering.html#2.5.1). For mostly QA reasons, we currently treat a DOI with an "en dash" as invalid. | |||||
* | ingest: improve tests, support old ingest results | Bryan Newbold | 2020-01-15 | 4 | -4/+30 | |
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* | update ingest worker for schema tweaks | Bryan Newbold | 2020-01-15 | 1 | -8/+15 | |
| | | | | | | Should be backwards compatible with old ingest results. Fixed a bug with glutton ident detection. | |||||
* | ingest: allow more sources to auto-import | Bryan Newbold | 2020-01-15 | 1 | -1/+2 | |
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* | datacite: skip records without a doi | Martin Czygan | 2020-01-13 | 1 | -0/+4 | |
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* | add missing sentry/raven tags | Bryan Newbold | 2020-01-10 | 3 | -2/+19 | |
| | | | | | | Good to have exceptions tracked and stored even for commands run from the command line. But in particular the importer runs as a kafka worker and should be tracking excpetions. | |||||
* | datacite: add entry to license slug map | Martin Czygan | 2020-01-09 | 2 | -0/+2 | |
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* | datacite: ignore known unknown values in resourceType* | Martin Czygan | 2020-01-09 | 4 | -3/+97 | |
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* | datacite: abstracts may be strings or list of strings | Martin Czygan | 2020-01-09 | 6 | -3/+202 | |
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* | datacite: improve license_slug handling | Martin Czygan | 2020-01-09 | 4 | -62/+134 | |
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* | datacite: add 'Unknown' to blacklist | Martin Czygan | 2020-01-09 | 2 | -8/+6 | |
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* | datacite: get rid of schemaVersion | Martin Czygan | 2020-01-09 | 18 | -35/+14 | |
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* | update deps | Martin Czygan | 2020-01-08 | 1 | -86/+69 | |
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* | Merge branch 'martin-datacite-import' | Martin Czygan | 2020-01-08 | 64 | -5/+5736 | |
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Pipfile.lock is broken. * martin-datacite-import: (68 commits) datacite: pass in doi into factored out method datacite: reformat test cases and use jq . --sort-keys datacite: factor out contributor handling datacite: catch type mismatch in language detection datacite: adjust tests for release_month datacite: name extra.month, extra.release_month datacite: mark additional files as stub datacite: CCDC are entries, mostly datacite: use more specific release_type, if possible datacite: ignore certain names datacite: over 3% records have the same title: stub datacite: fill a few more release_type gaps datacite: adding datacite-specific extra metadata datacite: apply pylint suggestions datacite: fix typos datacite: set release_stage to published by default datacite: month field should be top-level datacite: include month in extra datacite: indicate mismatched file in test datacite: clean abstracts, use unknown value tokens ... | |||||
| * | datacite: pass in doi into factored out method | Martin Czygan | 2020-01-08 | 1 | -2/+3 | |
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| * | datacite: reformat test cases and use jq . --sort-keys | Martin Czygan | 2020-01-08 | 54 | -2299/+2301 | |
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| * | datacite: factor out contributor handling | Martin Czygan | 2020-01-08 | 6 | -82/+210 | |
| | | | | | | | | | | | | | | Use values from: * attributes.creators[] * attributes.contributors[] | |||||
| * | datacite: catch type mismatch in language detection | Martin Czygan | 2020-01-08 | 1 | -3/+2 | |
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| * | datacite: adjust tests for release_month | Martin Czygan | 2020-01-08 | 12 | -12/+12 | |
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| * | datacite: name extra.month, extra.release_month | Martin Czygan | 2020-01-08 | 1 | -1/+3 | |
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| * | datacite: mark additional files as stub | Martin Czygan | 2020-01-08 | 4 | -1/+77 | |
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