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| author | Bryan Newbold <bnewbold@robocracy.org> | 2019-05-16 13:53:15 -0700 |
|---|---|---|
| committer | Bryan Newbold <bnewbold@robocracy.org> | 2019-05-21 11:41:29 -0700 |
| commit | 6ff79f47c7c7ae27b28685674672e58b7dd4d271 (patch) | |
| tree | 2470f89de864207da8ccc92151cb35d5e20ba21b /python/fatcat_tools/importers/pubmed.py | |
| parent | 300665927f578151321b0d91b28f8aadffcf227d (diff) | |
| download | fatcat-6ff79f47c7c7ae27b28685674672e58b7dd4d271.tar.gz fatcat-6ff79f47c7c7ae27b28685674672e58b7dd4d271.zip | |
tweaks to new imports/tests
Diffstat (limited to 'python/fatcat_tools/importers/pubmed.py')
| -rw-r--r-- | python/fatcat_tools/importers/pubmed.py | 10 |
1 files changed, 4 insertions, 6 deletions
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index 1feb41cd..f83922a3 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -115,9 +115,6 @@ class PubmedImporter(EntityImporter): XXX: full author names """ - def __init__(self): - pass - def __init__(self, api, issn_map_file, **kwargs): eg_desc = kwargs.get('editgroup_description', @@ -181,7 +178,8 @@ class PubmedImporter(EntityImporter): pmcid = identifiers.find("ArticleId", IdType="pmc") if pmcid: - pmcid = pmcid.string + # XXX: strip the version part? or retain? + pmcid = pmcid.string.split('.')[0] release_type = None pub_types = [] @@ -471,7 +469,7 @@ class PubmedImporter(EntityImporter): self.counts['exists-pmid-doi-mismatch'] += 1 return False - if existing and existing.ext_ids.pmid and existing.refs: + if existing and existing.ext_ids.pmid and (existing.refs or not re.refs): # TODO: any other reasons to do an update? # don't update if it already has PMID self.counts['exists'] += 1 @@ -508,5 +506,5 @@ class PubmedImporter(EntityImporter): #sys.exit(-1) if __name__=='__main__': - parser = PubMedParser() + parser = PubmedImporter(None, None) parser.parse_file(open(sys.argv[1])) |