def implementation(logger, host, user, passwd, args):
action_setup_conf = Recorder.find_action_setup_conf(args)
f = csv.DictReader(args.ifile, delimiter='\t')
records = [r for r in f]
if len(records) == 0:
msg = 'No records are going to be imported'
logger.critical(msg)
raise core.ImporterValidationError(msg)
canonizer = core.RecordCanonizer(['study'], args)
canonizer.canonize_list(records)
study_label = records[0]['study']
o = csv.DictWriter(args.ofile,
fieldnames=['study', 'label', 'type', 'vid'],
delimiter='\t',
lineterminator=os.linesep)
recorder = Recorder(o,
study_label,
host,
user,
passwd,
args.keep_tokens,
args.batch_size,
operator=args.operator,
action_setup_conf=action_setup_conf,
logger=logger)
report_fnames = copy.deepcopy(f.fieldnames)
report_fnames.append('error')
report = csv.DictWriter(args.report_file,
report_fnames,
delimiter='\t',
lineterminator=os.linesep,
extrasaction='ignore')
report.writeheader()
records, bad_records = recorder.do_consistency_checks(records)
for br in bad_records:
report.writerow(br)
if args.blocking_validator and len(bad_records) >= 1:
args.ofile.close()
args.ifile.close()
args.report_file.close()
msg = '%d invalid records' % len(bad_records)
recorder.logger.critical(msg)
raise core.ImporterValidationError(msg)
by_label = make_ind_by_label(records)
import_pedigree(recorder, by_label.itervalues())
recorder.clean_up()
args.ofile.close()
args.ifile.close()
args.report_file.close()
def implementation(logger, host, user, passwd, args):
action_setup_conf = Recorder.find_action_setup_conf(args)
f = csv.DictReader(args.ifile, delimiter='\t')
records = [r for r in f]
if len(records) == 0:
msg = 'No records are going to be imported'
logger.critical(msg)
raise core.ImporterValidationError(msg)
canonizer = core.RecordCanonizer(['study'], args)
canonizer.canonize_list(records)
study_label = records[0]['study']
o = csv.DictWriter(args.ofile, fieldnames=['study', 'label', 'type', 'vid'],
delimiter='\t', lineterminator=os.linesep)
recorder = Recorder(o, study_label, host, user, passwd,
args.keep_tokens, args.batch_size,
operator=args.operator,
action_setup_conf=action_setup_conf, logger=logger)
report_fnames = copy.deepcopy(f.fieldnames)
report_fnames.append('error')
report = csv.DictWriter(args.report_file, report_fnames,
delimiter='\t', lineterminator=os.linesep,
extrasaction='ignore')
report.writeheader()
records, bad_records = recorder.do_consistency_checks(records)
for br in bad_records:
report.writerow(br)
if args.blocking_validator and len(bad_records) >= 1:
args.ofile.close()
args.ifile.close()
args.report_file.close()
msg = '%d invalid records' % len(bad_records)
recorder.logger.critical(msg)
raise core.ImporterValidationError(msg)
by_label = make_ind_by_label(records)
import_pedigree(recorder, by_label.itervalues())
recorder.clean_up()
args.ofile.close()
args.ifile.close()
args.report_file.close()
def test_import_pedigree(self):
with open(os.path.join(DATA_DIR, "individuals.tsv")) as f:
reader = csv.DictReader(f, delimiter='\t')
records = [r for r in reader]
by_label = make_ind_by_label(records)
ped.import_pedigree(Recorder(), by_label.itervalues())
def test_import_pedigree(self):
with open(os.path.join(DATA_DIR, "individuals.tsv")) as f:
reader = csv.DictReader(f, delimiter='\t')
records = [r for r in reader]
by_label = make_ind_by_label(records)
ped.import_pedigree(Recorder(), by_label.itervalues())