Commit message (Collapse) | Author | Age | Files | Lines | |
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* | ingest importer: pass through link rel | Bryan Newbold | 2020-02-18 | 1 | -1/+6 |
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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. | ||||
* | Merge branch 'martin-harvest-print' into 'master' | bnewbold | 2020-02-14 | 3 | -17/+22 |
|\ | | | | | | | | | harvest: log state on startup and use stderr for diagnostics See merge request webgroup/fatcat!27 | ||||
| * | 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. | ||||
* | Merge branch 'martin-datacite-strptime-none' into 'master' | Martin Czygan | 2020-01-31 | 1 | -1/+1 |
|\ | | | | | | | | | datacite: prevent none See merge request webgroup/fatcat!25 | ||||
| * | datacite: prevent none | Martin Czygan | 2020-01-31 | 1 | -1/+1 |
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* | Merge branch 'martin-datacite-micropub' into 'master' | Martin Czygan | 2020-01-31 | 4 | -25/+162 |
|\ | | | | | | | | | datacite: improve date handling and minor tweak See merge request webgroup/fatcat!24 | ||||
| * | 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 | ||||
* | more TODO/proposal cleanup | Bryan Newbold | 2020-01-22 | 4 | -10/+34 |
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* | more details on potential _edit table disk savings | Bryan Newbold | 2020-01-22 | 1 | -3/+23 |
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* | proposal of ideas for reducing database size | Bryan Newbold | 2020-01-21 | 1 | -0/+154 |
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* | cleanup some of old TODO list into proposals | Bryan Newbold | 2020-01-21 | 4 | -44/+269 |
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* | 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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* | stats: remove internal PG table sizes from old dumps | Bryan Newbold | 2020-01-19 | 2 | -292/+0 |
| | | | | For ease of reading and comparison | ||||
* | update stats and table sizes | Bryan Newbold | 2020-01-19 | 4 | -0/+96 |
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* | Merge branch 'martin-openapi-typo-exmaple' into 'master' | bnewbold | 2020-01-19 | 1 | -1/+1 |
|\ | | | | | | | | | fix a typo in openapi definition See merge request webgroup/fatcat!20 | ||||
| * | fix a typo in openapi definition | Martin Czygan | 2020-01-18 | 1 | -1/+1 |
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* | | Merge branch 'martin-guide-typos-sentance' into 'master' | bnewbold | 2020-01-19 | 1 | -2/+2 |
|\ \ | | | | | | | | | | | | | fix two typos in editing guide See merge request webgroup/fatcat!21 | ||||
| * | | fix two typos in editing guide | Martin Czygan | 2020-01-18 | 1 | -2/+2 |
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* | | basic notes in bulk edit changelog | Bryan Newbold | 2020-01-19 | 1 | -0/+7 |
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* | | bulk edit notes for datacite (QA) | Bryan Newbold | 2020-01-19 | 1 | -0/+152 |
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* | | pubmed update notes | Bryan Newbold | 2020-01-19 | 1 | -1/+46 |
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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-openapi-typos' into 'master' | Martin Czygan | 2020-01-19 | 1 | -2/+2 |
|\ \ | |/ |/| | | | | | fix typos in openapi spec descriptions See merge request webgroup/fatcat!22 | ||||
| * | fix typos in openapi spec descriptions | Martin Czygan | 2020-01-19 | 1 | -2/+2 |
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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! | ||||
* | | yet more schema update ideas | Bryan Newbold | 2020-01-17 | 1 | -2/+4 |
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* | | actually control pubmed updates with a flag | Bryan Newbold | 2020-01-17 | 1 | -0/+4 |
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* | | Merge branch 'bnewbold-abstracts-corner-case' into 'master' | bnewbold | 2020-01-17 | 1 | -1/+4 |
|\ \ | | | | | | | | | | | | | fatcatd: fix corner-case in abstracts insertion See merge request webgroup/fatcat!17 |