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* entity worker: ingest more releasesBryan Newbold2020-02-221-1/+37
| | | | | | | | If release is a dataset or image, don't do a pdf ingest request. If release is a datacite DOI, and release_type is a "document", crawl regardless of is_oa detection. This is mostly to crawl repositories (institutional or subject).
* Merge branch 'bnewbold-shadow-import'Bryan Newbold2020-02-192-0/+196
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| * remove arabesque short wayback URL hackBryan Newbold2020-02-141-6/+0
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| * improve shadow import file url cleanup pathBryan Newbold2020-02-131-2/+12
| | | | | | | | Should probably be refactored out in to shared cleanup code.
| * shadow import fixes from QA testingBryan Newbold2020-02-131-0/+6
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| * shadow import: more filtering of file_meta fieldsBryan Newbold2020-02-131-0/+10
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| * basic shadow importerBryan Newbold2020-02-132-0/+176
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* | always crawl researchgate DOIsBryan Newbold2020-02-181-0/+2
| | | | | | | | Now that ingest is fixed
* | ingest import: fix edit_extra pathBryan Newbold2020-02-181-1/+1
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* | ingest importer: edit_extra is a top-level keyBryan Newbold2020-02-181-1/+1
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* | ingest import: allow short version of corpus namesBryan Newbold2020-02-181-0/+3
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* | ingest importer: pass through link relBryan Newbold2020-02-181-1/+6
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* | harvest: log state on startup and use stderr for diagnosticsMartin Czygan2020-02-143-17/+22
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* add acceptlist override for biorxiv/medrxivBryan Newbold2020-02-101-2/+12
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* check ingest_request_source existance for SPN as well as ingestBryan Newbold2020-02-061-0/+3
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* additional trusted link sourcesBryan Newbold2020-02-061-0/+3
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* add mag and s2 as trusted link sourcesBryan Newbold2020-02-061-1/+1
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* ingest worker: handle missing ingest_request_sourceBryan Newbold2020-02-061-0/+3
| | | | | Seeing a bunch of these due to re-ingests not including this field because of an earlier persist bug.
* 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.
* datacite: prevent noneMartin Czygan2020-01-311-1/+1
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* datacite: name shall not be NoneMartin Czygan2020-01-311-1/+1
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* datacite: add exception for https://www.micropublication.org/Martin Czygan2020-01-311-0/+5
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* datacite: do not skip records w/o dateMartin Czygan2020-01-311-2/+1
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* datacite: improve docstringMartin Czygan2020-01-311-4/+4
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* datacite: improve date handling and minor tweakMartin Czygan2020-01-301-19/+42
| | | | | | | | | | | | | 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 errorsBryan Newbold2020-01-293-3/+3
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* additional DOI prefix filtersBryan Newbold2020-01-281-0/+8
| | | | From martin, thanks.
* apply ingest request filtering in entity workerBryan Newbold2020-01-281-3/+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 transformBryan Newbold2020-01-281-14/+1
| | | | Refactoring to move this filter elsewhere
* fix trivial typo in file importerBryan Newbold2020-01-201-1/+1
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* normal: DOI corner-case from pubmed importBryan Newbold2020-01-191-0/+9
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* do not normalize "en dash" in DOIMartin Czygan2020-01-171-2/+5
| | | | | | | | | 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 resultsBryan Newbold2020-01-151-3/+12
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* update ingest worker for schema tweaksBryan Newbold2020-01-151-8/+15
| | | | | | Should be backwards compatible with old ingest results. Fixed a bug with glutton ident detection.
* ingest: allow more sources to auto-importBryan Newbold2020-01-151-1/+2
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* datacite: skip records without a doiMartin Czygan2020-01-131-0/+4
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* datacite: add entry to license slug mapMartin Czygan2020-01-091-0/+1
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* datacite: ignore known unknown values in resourceType*Martin Czygan2020-01-091-2/+2
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* datacite: abstracts may be strings or list of stringsMartin Czygan2020-01-091-2/+15
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* datacite: improve license_slug handlingMartin Czygan2020-01-091-60/+101
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* datacite: add 'Unknown' to blacklistMartin Czygan2020-01-091-1/+5
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* datacite: get rid of schemaVersionMartin Czygan2020-01-091-3/+0
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* Merge branch 'martin-datacite-import'Martin Czygan2020-01-082-0/+1024
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 methodMartin Czygan2020-01-081-2/+3
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| * datacite: factor out contributor handlingMartin Czygan2020-01-081-80/+103
| | | | | | | | | | | | | | Use values from: * attributes.creators[] * attributes.contributors[]
| * datacite: catch type mismatch in language detectionMartin Czygan2020-01-081-3/+2
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| * datacite: name extra.month, extra.release_monthMartin Czygan2020-01-081-1/+3
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| * datacite: mark additional files as stubMartin Czygan2020-01-081-0/+4
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| * datacite: CCDC are entries, mostlyMartin Czygan2020-01-081-0/+4
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| * datacite: use more specific release_type, if possibleMartin Czygan2020-01-081-0/+6
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