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)