diff options
Diffstat (limited to 'python/fatcat_tools/importers/pubmed.py')
| -rw-r--r-- | python/fatcat_tools/importers/pubmed.py | 27 |
1 files changed, 26 insertions, 1 deletions
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index c32ce34a..3ecf5ef4 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -616,7 +616,10 @@ class PubmedImporter(EntityImporter): ### References refs = [] if pubmed.ReferenceList: - for ref in pubmed.ReferenceList.find_all('Reference'): + # note that Reference always exists within a ReferenceList, but + # that there may be multiple ReferenceList (eg, sometimes one per + # Reference) + for ref in pubmed.find_all('Reference'): ref_extra = dict() ref_doi = ref.find("ArticleId", IdType="doi") if ref_doi: @@ -729,8 +732,29 @@ 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 +764,7 @@ 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 |