Re-initiate testing for individual sub-commands of the SRAweb module

[saketkc]

Re-initiate testing for individual sub-commands of the SRAweb module

[dibyaaaaax]

Hi, I would like to take up this issue but I am facing a problem.
How do I write a command to make sure SRAweb is used instead of SRAmetadb? All the command I have tried initiates the download process for SRAmetadb.sqlite.gz.

[saketkc]

Hi @dibyaaaaax, thanks for your interest! I just added a template version for testing SRAweb mode here: https://github.com/saketkc/pysradb/blob/master/tests/test_sraweb.py

The idea would be to test each and every function that is in sraweb.py. Ideally, each function should be tested on different set of SRP IDs. I have attached a list of SRPs in a file here. In order to verify if the total number of records for each SRP are correct, you will need to manually verify it using the web interface.

Example:

SRP: SRP016501
Online version of metadata (URL): https://www.ncbi.nlm.nih.gov/Traces/study1/?acc=SRP016501

1.Basic check:
Verify that the total number of records is 134 as shown under the "Runs" column.

2.Advanced check:
Check if the tissue column in the online version is the same as in the SRAweb version when using sraweb_connection.sra_metadata("SRP016501", detailed=True). One easy way to do this is to download the "Runinfo table" from SRA (using the URL above, also attached here) and check if SRAweb's output captures all the columns in the Runinfo table or not (even if the exact column name is not the same).

Please let me know if you have any questions.
SRP_IDs.txt
SraRunTable.txt

[saketkc]

Should be fixed by #43