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authorBryan Newbold <bnewbold@robocracy.org>2019-12-23 18:14:07 -0800
committerBryan Newbold <bnewbold@robocracy.org>2019-12-23 18:18:40 -0800
commitf9ffc6d99c53a2ead4b3486e25f0342b6ebc5cdc (patch)
treeb13f19a3c8d4e1a847adbe04b701da6c1258f14c /python/fatcat_tools
parent05ce151586ec69edc8450ea7d901045798de19f6 (diff)
downloadfatcat-f9ffc6d99c53a2ead4b3486e25f0342b6ebc5cdc.tar.gz
fatcat-f9ffc6d99c53a2ead4b3486e25f0342b6ebc5cdc.zip
pubmed: improve warning and stderr formatting
Diffstat (limited to 'python/fatcat_tools')
-rw-r--r--python/fatcat_tools/importers/pubmed.py11
1 files changed, 6 insertions, 5 deletions
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py
index ced78d5d..8019e36a 100644
--- a/python/fatcat_tools/importers/pubmed.py
+++ b/python/fatcat_tools/importers/pubmed.py
@@ -466,17 +466,17 @@ class PubmedImporter(EntityImporter):
int(pub_date.Day.string))
release_date = release_date.isoformat()
except ValueError as ve:
- sys.stderr.write("bad date, skipping: {}\n".format(ve))
+ print("bad date, skipping: {}".format(ve), file=sys.stderr)
release_date = None
elif pub_date.MedlineDate:
medline_date = pub_date.MedlineDate.string.strip()
if len(medline_date) >= 4 and medline_date[:4].isdigit():
release_year = int(medline_date[:4])
if release_year < 1300 or release_year > 2040:
- print("bad medline year, skipping: {}\n".format(release_year), file=sys.stderr)
+ print("bad medline year, skipping: {}".format(release_year), file=sys.stderr)
release_year = None
else:
- print("unparsable medline date, skipping: {}\n".format(medline_date), file=sys.stderr)
+ print("unparsable medline date, skipping: {}".format(medline_date), file=sys.stderr)
if journal.find("Title"):
container_name = journal.Title.string
@@ -708,8 +708,9 @@ class PubmedImporter(EntityImporter):
if err.status != 404:
raise err
if existing and existing.ext_ids.pmid and existing.ext_ids.pmid != re.ext_ids.pmid:
- warnings.warn("PMID/DOI mismatch: release {}, pmid {} != {}".format(
- existing.ident, existing.ext_ids.pmid, re.ext_ids.pmid))
+ warn_str = "PMID/DOI mismatch: release {}, pmid {} != {}".format(
+ existing.ident, existing.ext_ids.pmid, re.ext_ids.pmid)
+ warnings.warn(warn_str)
self.counts['warn-pmid-doi-mismatch'] += 1
# don't clobber DOI, but do group together
re.ext_ids.doi = None