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| author | Bryan Newbold <bnewbold@robocracy.org> | 2020-03-19 23:37:27 -0700 |
|---|---|---|
| committer | Bryan Newbold <bnewbold@robocracy.org> | 2020-03-19 23:46:45 -0700 |
| commit | 12c0e53669fb9401b09e088217c5c103d90b9106 (patch) | |
| tree | df3acd46019bff5fc5b8a1d901f73df707c39556 | |
| parent | c1c620640a821589882d50ecbb31b1ff743ec26d (diff) | |
| download | fatcat-12c0e53669fb9401b09e088217c5c103d90b9106.tar.gz fatcat-12c0e53669fb9401b09e088217c5c103d90b9106.zip | |
pubmed: update many more metadata fields
In particular, with daily updates in most cases the DOI will be
registered first, then the entity updated with PMID when that is
available. Often the pubmed metadata will be more complete, with
abstracts etc, and we'll want those improvements.
| -rw-r--r-- | python/fatcat_tools/importers/pubmed.py | 22 |
1 files changed, 22 insertions, 0 deletions
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index c32ce34a..70a6368d 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -729,8 +729,29 @@ class PubmedImporter(EntityImporter): existing.ext_ids.doi = existing.ext_ids.doi or re.ext_ids.doi existing.ext_ids.pmid = existing.ext_ids.pmid or re.ext_ids.pmid existing.ext_ids.pmcid = existing.ext_ids.pmcid or re.ext_ids.pmcid + + existing.container_id = existing.container_id or re.container_id existing.refs = existing.refs or re.refs + existing.abstracts = existing.abstracts or re.abstracts existing.extra['pubmed'] = re.extra['pubmed'] + + # fix stub titles + if existing.title in [ + "OUP accepted manuscript", + ]: + existing.title = re.title + + existing.original_title = existing.original_title or re.original_title + existing.release_type = existing.release_type or re.release_type + existing.release_stage = existing.release_stage or re.release_stage + existing.release_date = existing.release_date or re.release_date + existing.release_year = existing.release_year or re.release_year + existing.withdrawn_status = existing.withdrawn_status or re.withdrawn_status + existing.volume = existing.volume or re.volume + existing.issue = existing.issue or re.issue + existing.pages = existing.pages or re.pages + existing.language = existing.language or re.language + # update subtitle in-place first if not existing.subtitle and existing.extra.get('subtitle'): subtitle = existing.extra.pop('subtitle') @@ -740,6 +761,7 @@ class PubmedImporter(EntityImporter): existing.subtitle = subtitle if not existing.subtitle: existing.subtitle = re.subtitle + try: self.api.update_release(self.get_editgroup_id(), existing.ident, existing) self.counts['update'] += 1 |