Describe the bug
The gsm-to-gse subcommand fails with an error.
To Reproduce
Steps to reproduce the behavior:
pysradb gsm-to-gse GSM3396533 fails but all of
pysradb gsm-to-srr GSM3396533pysradb gsm-to-srx GSM3396533pysradb gsm-to-srs GSM3396533pysradb gsm-to-srp GSM3396533 work perfectly fine.
This is because there is no gsm_to_gse() function in sraweb.py but the others have their functions in there.
This is the traceback:
Traceback (most recent call last):<br/>
File "/usr/local/bin/pysradb", line 8, in <module>
sys.exit(parse_args())
File "/usr/local/lib/python3.7/dist-packages/pysradb/cli.py", line 1223, in parse_args
gsm_to_gse(args.gsm_ids, args.saveto, args.detailed, args.desc, args.expand)
File "/usr/local/lib/python3.7/dist-packages/pysradb/cli.py", line 254, in gsm_to_gse
expand_sample_attributes=expand,
File "/usr/local/lib/python3.7/dist-packages/pysradb/sradb.py", line 793, in gsm_to_gse
df = self.query(sql)
File "/usr/local/lib/python3.7/dist-packages/pysradb/basedb.py", line 108, in query
results = self.cursor.execute(sql_query).fetchall()
AttributeError: 'SRAweb' object has no attribute 'cursor'
Desktop (please complete the following information):
OS: [e.g. Ubuntu 18.04]
Python version [e.g. 3.7.5]
I have added the following function in class SRAweb that makes it work:
Describe the bug The gsm-to-gse subcommand fails with an error.
To Reproduce Steps to reproduce the behavior:
pysradb gsm-to-gse GSM3396533
fails but all ofpysradb gsm-to-srr GSM3396533
pysradb gsm-to-srx GSM3396533
pysradb gsm-to-srs GSM3396533
pysradb gsm-to-srp GSM3396533
work perfectly fine.This is because there is no gsm_to_gse() function in sraweb.py but the others have their functions in there.
This is the traceback:
Desktop (please complete the following information):
I have added the following function in
class SRAweb
that makes it work:I can create a pull request if you'd like.