diff options
Diffstat (limited to 'python/fatcat_tools/importers/pubmed.py')
| -rw-r--r-- | python/fatcat_tools/importers/pubmed.py | 31 |
1 files changed, 14 insertions, 17 deletions
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index 59b65b19..ced78d5d 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -8,6 +8,7 @@ from bs4 import BeautifulSoup from bs4.element import NavigableString import fatcat_openapi_client +from fatcat_tools.normal import * from .common import EntityImporter, clean, LANG_MAP_MARC # from: https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.publication_types/?report=objectonly @@ -348,19 +349,13 @@ class PubmedImporter(EntityImporter): pmid = medline.PMID.string.strip() doi = identifiers.find("ArticleId", IdType="doi") if doi and doi.string: - doi = doi.string.lower().strip() - if doi.startswith('doi:'): - doi = doi[4:] - if not (doi.startswith('10.') and '/' in doi and doi.split('/')[1]) and len(doi.split()) == 1: - sys.stderr.write("BOGUS DOI: {}\n".format(doi)) - doi = None + doi = clean_doi(doi.string) + else: + doi = None pmcid = identifiers.find("ArticleId", IdType="pmc") if pmcid: - pmcid = pmcid.string.strip().upper() - # got a bunch of weird ones like "wst_2018_399" in the 2019 baseline - if not pmcid.startswith("PMC"): - pmcid = None + pmcid = clean_pmcid(pmcid.string.strip().upper()) release_type = None pub_types = [] @@ -623,19 +618,21 @@ class PubmedImporter(EntityImporter): if pubmed.ReferenceList: for ref in pubmed.ReferenceList.find_all('Reference'): ref_extra = dict() - ref_pmid = ref.find("ArticleId", IdType="pubmed") ref_doi = ref.find("ArticleId", IdType="doi") - ref_release_id = None + if ref_doi: + ref_doi = clean_doi(ref_doi.string) + ref_pmid = ref.find("ArticleId", IdType="pubmed") if ref_pmid: - ref_pmid = ref_pmid.string.strip() - ref_extra['pmid'] = ref_pmid - if self.lookup_refs: - ref_release_id = self.lookup_pmid(ref_pmid) + ref_pmid = clean_pmid(ref_pmid.string) + ref_release_id = None if ref_doi: - ref_doi = ref_doi.string.lower().strip() ref_extra['doi'] = ref_doi if self.lookup_refs: ref_release_id = self.lookup_doi(ref_doi) + if ref_pmid: + ref_extra['pmid'] = ref_pmid + if self.lookup_refs: + ref_release_id = self.lookup_pmid(ref_pmid) ref_raw = ref.Citation if ref_raw: ref_extra['unstructured'] = ref_raw.string |