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authorBryan Newbold <bnewbold@robocracy.org>2019-12-23 18:09:31 -0800
committerBryan Newbold <bnewbold@robocracy.org>2019-12-23 18:18:26 -0800
commitcf62de67f788f19efb629413376eb2502d85d041 (patch)
tree46eb312831ec95c8b4aa82e688bb0c963be22b7e /python/fatcat_tools
parentb7b5e56b55d9699e5882b77293228375bd6099cf (diff)
downloadfatcat-cf62de67f788f19efb629413376eb2502d85d041.tar.gz
fatcat-cf62de67f788f19efb629413376eb2502d85d041.zip
pubmed: remove unused extid mapping code
Diffstat (limited to 'python/fatcat_tools')
-rw-r--r--python/fatcat_tools/importers/pubmed.py29
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