cursor.execute("""
SELECT uid
FROM queued_records
""")
rows = cursor.fetchall()
parser = Parser(pubmed_source)
for row in rows:
qr = QueuedRecord(context, row[0])
print 'Fetching pubmed data for ui %s' % qr.unique_identifier
pm_data = pubmed_search.fetch(qr.unique_identifier)
fetched_records = parser.parse(mapped_terms=complete_mapping,
is_email=False, data=pm_data)
if len(fetched_records) != 1:
print 'Fetch for %s (%s) found %s records, ignoring' % (ui,
qr.uid, len(fetched_records))
else:
print 'Orig metadata:', qr.metadata
fetched_rec = fetched_records[0]
print 'Fetched metadata:', fetched_rec.metadata
fetched_rec_metadata = fetched_rec.get_mapped_metadata(complete_mapping)
print 'Fetched metadata, mapped:', fetched_rec_metadata
if options.update:
print 'Updating.'
qr.metadata = fetched_rec.metadata
qr.save(context)
# It is a condition of Entrez eutilities to wait 3s bet. requests
time.sleep(3)
FROM queued_records
""")
rows = cursor.fetchall()
parser = Parser(pubmed_source)
for row in rows:
qr = QueuedRecord(context, row[0])
print 'Fetching pubmed data for ui %s' % qr.unique_identifier
pm_data = pubmed_search.fetch(qr.unique_identifier)
fetched_records = parser.parse(mapped_terms=complete_mapping,
is_email=False,
data=pm_data)
if len(fetched_records) != 1:
print 'Fetch for %s (%s) found %s records, ignoring' % (
ui, qr.uid, len(fetched_records))
else:
print 'Orig metadata:', qr.metadata
fetched_rec = fetched_records[0]
print 'Fetched metadata:', fetched_rec.metadata
fetched_rec_metadata = fetched_rec.get_mapped_metadata(
complete_mapping)
print 'Fetched metadata, mapped:', fetched_rec_metadata
if options.update:
print 'Updating.'
qr.metadata = fetched_rec.metadata
qr.save(context)
# It is a condition of Entrez eutilities to wait 3s bet. requests
time.sleep(3)
