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I have list of GEO study accession IDs and need to extract SRA meta data. And I got several studies returned error message. Does anyone know what causes this issue?
These are the GSEs causing errors:
GSE37005
GSE29714
GSE47217
GSE54365
GSE113801
GSE115106
GSE108333
GSE123527
GSE130894
GSE134964
GSE133600
GSE182269
GSE163140
To Reproduce
Steps to reproduce the behavior: pysradb gse-to-srp GSE37005
Error message
Traceback (most recent call last):
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/requests/models.py", line 971, in json
return complexjson.loads(self.text, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/bin/pysradb", line 10, in <module>
sys.exit(parse_args())
^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/pysradb/cli.py", line 1206, in parse_args
gse_to_srp(args.gse_ids, args.saveto, args.detailed, args.desc, args.expand)
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/pysradb/cli.py", line 232, in gse_to_srp
df = sradb.gse_to_srp(
^^^^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/pysradb/sraweb.py", line 793, in gse_to_srp
srp_df = self.srx_to_srp(srx)
^^^^^^^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/pysradb/sraweb.py", line 977, in srx_to_srp
srx_df = self.sra_metadata(srx, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/pysradb/sraweb.py", line 415, in sra_metadata
esummary_result = self.get_esummary_response("sra", srp)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/pysradb/sraweb.py", line 309, in get_esummary_response
response = _retry_response(self.base_url["esummary"], payload, "result")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/pysradb/sraweb.py", line 46, in _retry_response
response = request.json()
^^^^^^^^^^^^^^
File "/ihome/yufeihuang/suj40/Downloads/enter/envs/pysradb/lib/python3.11/site-packages/requests/models.py", line 975, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Thanks for the help in advance!
The text was updated successfully, but these errors were encountered:
Thanks for pointing these out. I can confirm that they error out but currently do not exactly understand why. I will try to debug it over the next few days.
Hello,
I have list of GEO study accession IDs and need to extract SRA meta data. And I got several studies returned error message. Does anyone know what causes this issue?
These are the GSEs causing errors:
GSE37005
GSE29714
GSE47217
GSE54365
GSE113801
GSE115106
GSE108333
GSE123527
GSE130894
GSE134964
GSE133600
GSE182269
GSE163140
To Reproduce
Steps to reproduce the behavior:
pysradb gse-to-srp GSE37005
Error message
Thanks for the help in advance!
The text was updated successfully, but these errors were encountered: