search

J-81 / dp_tools

MIT License
1 stars 7 forks source link

links to download multiqc files seem to be broken #32

Open asaravia-butler opened 10 months ago

asaravia-butler commented 10 months ago

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 commented 10 months ago

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?