Describe the bug
Missing run-related data for experiments having many runs. When I run pysradb metadata SRP245574, certain rows have missing entries for run_accession, run_total_spots, run_total_bases. I don't think this part is a bug per se as those data are really missing in the response from NCBI given by the function get_esummary_response. It seems that this missing information happens for experiments that have many runs (not sure the threshold). However, those data are accessible using get_efetch_response, which is used when --detailed is selected. Because of this, in SRAweb.sra_metadata, I believed the merging of results from get_esummary_response and get_efetch_response is not generating a dataframe we expect. For example, pysradb metadata --detailed SRP245574 outputs a table with many rows with missing experiment accession. Those rows correspond to the runs which were not included in the results from get_esummary_response but included in those from get_efetch_response.
To Reproduce
Steps to reproduce the behavior:
pysradb metadata SRP245574pysradb metadata --detailed SRP245574
Desktop :
OS: Linux MSI 5.15.133.1-microsoft-standard-WSL2
Python version: 3.10
Additional context
I would like to work on this issue if it is okay.
Describe the bug Missing run-related data for experiments having many runs. When I run
pysradb metadata SRP245574, certain rows have missing entries forrun_accession,run_total_spots,run_total_bases. I don't think this part is a bug per se as those data are really missing in the response from NCBI given by the functionget_esummary_response. It seems that this missing information happens for experiments that have many runs (not sure the threshold). However, those data are accessible usingget_efetch_response, which is used when--detailedis selected. Because of this, inSRAweb.sra_metadata, I believed the merging of results fromget_esummary_responseandget_efetch_responseis not generating a dataframe we expect. For example,pysradb metadata --detailed SRP245574outputs a table with many rows with missing experiment accession. Those rows correspond to the runs which were not included in the results fromget_esummary_responsebut included in those fromget_efetch_response.To Reproduce Steps to reproduce the behavior:
pysradb metadata SRP245574pysradb metadata --detailed SRP245574Desktop :
Additional context I would like to work on this issue if it is okay.