Closed hh1985 closed 8 months ago
SSL errors are intermittent from NCBI end. I do not see it anymore:
$ pysradb metadata SRP000941 | head
study_accession study_title experiment_accession experiment_title experiment_desc organism_taxid organism_name library_name library_strategy library_source library_selection library_layout sample_accession sample_title biosample bioproject instrument instrument_model instrument_model_desc total_spots total_size run_accession run_total_spots run_total_bases
SRP000941 UCSD Human Reference Epigenome Mapping Project SRX027874 Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in hESC Cells Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in hESC Cells 9606 Homo sapiens LL218 ChIP-Seq GENOMIC ChIP SINGLE SRS006930 SAMN00004698 <NA> Illumina Genome Analyzer II Illumina Genome Analyzer II ILLUMINA 59041190 1555248627 SRR018453 11642838 419142168
Just a note: I used proxy. I followed suggestion in github and downgraded the urllib3 to 1.25.11. Problem solved.
conda install urllib3=1.25.11
Describe the bug Cannot extract the metadata with pysradb. Received SSLError:
To Reproduce Steps to reproduce the behavior:
pysradb metadata SRP000941 | head
orpysradb metadata SRP000941 --saveto test.tsv
Desktop (please complete the following information):
Additional context Tried the command on home and office computers. Received the same error.