Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

links to download multiqc files seem to be broken #32

Open
asaravia-butler opened this issue Oct 30, 2023 · 1 comment
Open

links to download multiqc files seem to be broken #32

asaravia-butler opened this issue Oct 30, 2023 · 1 comment

Comments

@asaravia-butler
Copy link

gitpod /workspace/dp_tools (metrics_extraction_subfeature) $ python download_multiqc_from_OSD.py --osd-id --output-dir
https://osdr.nasa.gov/genelab/data/glds/files/
Traceback (most recent call last):
File "/workspace/dp_tools/download_multiqc_from_OSD.py", line 54, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/download_multiqc_from_OSD.py", line 16, in main
files = find_matching_filenames(accession=osd_id, filename_pattern=".multiqc..zip")
File "/workspace/dp_tools/dp_tools/glds_api/commons.py", line 56, in find_matching_filenames
df = get_table_of_files(accession)
File "/workspace/dp_tools/dp_tools/glds_api/commons.py", line 41, in get_table_of_files
with urlopen(url) as response:
File "/home/gitpod/miniconda3/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/home/gitpod/miniconda3/lib/python3.10/urllib/request.py", line 525, in open
response = meth(req, response)
File "/home/gitpod/miniconda3/lib/python3.10/urllib/request.py", line 634, in http_response
response = self.parent.error(
File "/home/gitpod/miniconda3/lib/python3.10/urllib/request.py", line 563, in error
return self._call_chain(*args)
File "/home/gitpod/miniconda3/lib/python3.10/urllib/request.py", line 496, in _call_chain
result = func(*args)
File "/home/gitpod/miniconda3/lib/python3.10/urllib/request.py", line 643, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: NOT FOUND

@asaravia-butler
Copy link
Author

Looks like the example command just needs to be updated to require an OSD-#...
Is there a way to pull all OSD numbers that include RNAseq data without having to specify each one?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

2 participants