fastq's URLs are empty

[NomiCentarix]

Describe the bug
The columns "ena_fastq_http", "ena_fastq_http" and "ena_fastq_http" are all NA.
I tested the code in several environments, and no change.
(the data does exist in the same path as before
http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR236/077/SRR23630177/SRR23630177_1.fastq.gz)

To Reproduce

from pysradb.sraweb import SRAweb

db = SRAweb()
gse_to_srp = db.gse_to_srp("GSE226189")
print("gse_to_srp shape:", gse_to_srp.shape)
display(gse_to_srp.head(2))

metadata = db.sra_metadata(gse_to_srp["study_accession"].to_list(), detailed=True)
print(metadata.shape)
display(metadata.head(2))

Desktop (please complete the following information):

• OS: [e.g. Ubuntu 20.04]
• Python version [e.g. 3.8]

thanks

[saketkc]

Thanks for the bug report. It is possible something has changed at the EBI end. I will try to check.

[marcomoretto]

I think the bug is related to the concurrent part here

pysradb/pysradb/sraweb.py

Line 694 in 99d0ef7

with concurrent.futures.ThreadPoolExecutor(max_workers=5) as executor:

Calling fetch_ena_fastq works as expected and retrieve the correct URLs

from pysradb.sraweb import SRAweb
db = SRAweb()
db.fetch_ena_fastq("SRP059263")