def run(args): EcsEntry.objects.all().delete() parser = EcsFileParser(args[1]) try: inserter = BulkInserter(EcsEntry) while True: entries = parser.next_ecs_entry() if not entries: break for entry in entries: inserter.save(entry) inserter.close() except Exception: inserter.rollback() raise
def run(args):
try:
parser = geovision.text_to_db.sample_parser.SamplefileParser(args[1])
except IOError:
print "Unable to open file", args[1]
sys.exit(1);
if ImportedData.objects.filter(type='sample', data=parser.sample).exists():
print("Warning: Not importing sample %s because it already exists" % parser.sample)
sys.exit(1)
try:
inserter = BulkInserter(Read)
read_entry = parser.next_read()
while read_entry is not None:
inserter.save(read_entry)
read_entry = parser.next_read()
inserter.close()
ImportedData.objects.create(type='sample', data=parser.sample)
except Exception as e:
inserter.rollback()
raise
def run(args):
try:
parser = geovision.text_to_db.db_parser.DbfileParser(args[1], args[2])
except IOError:
print("Unable to open file", args[1])
sys.exit(1);
if ImportedData.objects.filter(type='dbentry', data=parser.source).exists():
print("Warning: Not importing database %s because it already exists" % args[2])
sys.exit(1)
try:
inserter = BulkInserter(DbEntry)
db_entry = parser.next_db_entry()
while db_entry is not None:
inserter.save(db_entry)
db_entry = parser.next_db_entry()
inserter.close()
ImportedData.objects.create(type='dbentry', data=parser.source)
except Exception as e:
inserter.rollback()
raise
(read_id, db_seq_id, pident, length, mismatch, gapopen, qstart, qend, sstart, send, error_value, bitscore, read_seq, db_seq) = line.split(None)
if db_name == 'uniprot':
db_seq_id = db_seq_id.split('|')[1]
id = inserter.get_id()
inserter.save(dict_from_kwargs(read_id=read_id, database_name=db_name, sample=sample_name, db_entry_id=db_seq_id, bitscore=bitscore, error_value=error_value))
extra_inserter.save(dict_from_kwargs(blast_id=id, pident=pident, length=length, mismatch=mismatch, gapopen=gapopen, qstart=qstart, qend=qend, sstart=sstart, send=send, read_seq=read_seq, db_seq=db_seq))
inserter.close()
extra_inserter.close()
if __name__ == '__main__':
import sys
filename = sys.argv[1]
(sample_name, db_name, rest) = os.path.basename(filename).split('.')
blast_name = sample_name + '.' + db_name
if ImportedData.objects.filter(type='blast', data=blast_name).exists():
print("Not importing blast %s because it already exists" % blast_name)
sys.exit(1)
if not ImportedData.objects.filter(type='sample', data=sample_name).exists():
print("Not importing blast %s because sample %s doesn't exist" % (blast_name, sample_name))
sys.exit(1)
if not ImportedData.objects.filter(type='dbentry', data=db_name).exists():
print("Not importing blast %s because database %s doesn't exist" % (blast_name, db_name))
sys.exit(1)
try:
create_blast(db_name, sample_name, filename)
ImportedData.objects.create(type='blast', data=blast_name)
except Exception as e:
inserter.rollback()
extra_inserter.rollback()
raise
