diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/fatcat_tools/importers/pubmed.py | 29 |
1 files changed, 0 insertions, 29 deletions
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index 1b2d4580..59b65b19 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -330,38 +330,9 @@ class PubmedImporter(EntityImporter): **kwargs) self.lookup_refs = lookup_refs - extid_map_file = kwargs.get('extid_map_file') - self.extid_map_db = None - if extid_map_file: - db_uri = "file:{}?mode=ro".format(extid_map_file) - print("Using external ID map: {}".format(db_uri)) - self.extid_map_db = sqlite3.connect(db_uri, uri=True) - else: - print("Not using external ID map") - self.create_containers = kwargs.get('create_containers', True) self.read_issn_map_file(issn_map_file) - def lookup_ext_ids(self, pmid): - if self.extid_map_db is None: - return dict(doi=None, core_id=None, pmid=None, pmcid=None, - wikidata_qid=None, arxiv_id=None, jstor_id=None) - row = self.extid_map_db.execute("SELECT core, doi, pmcid, wikidata FROM ids WHERE pmid=? LIMIT 1", - [pmid]).fetchone() - if row is None: - return dict(doi=None, core_id=None, pmid=None, pmcid=None, - wikidata_qid=None, arxiv_id=None, jstor_id=None) - row = [str(cell or '') or None for cell in row] - return dict( - core_id=row[0], - doi=row[1], - pmcid=row[2], - wikidata_qid=row[3], - # TODO: - arxiv_id=None, - jstor_id=None, - ) - def want(self, obj): return True |