Reviewer 1 - comment 2 - Cannot change the directory of downloaded Dataset files (using astropy)

[JonnyTran]

• openOmics version: 0.8.4
• Python version: 3.7.9
• Operating System: Ubuntu 20.04 - Linux 64

Description

Running gtex = GTEx(path="https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/") Results in: OSError: Not enough free space in /homes/.astropy/cache/download/url to download a 3.6G file, only 2.7G left.

Is there a possibility to choose the directory in which the files should be downloaded? This would be great.

What I Did

gtex = GTEx(path="https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/")

OSError: Not enough free space in /homes/.astropy/cache/download/url to download a 3.6G file, only 2.7G left.

[JonnyTran]

I suggested the following fix:

I used the package astropy to automatically cache downloaded files. It defaults to saving the files at /homes/.astropy/cache/, and ideally it should be in one location for each user-session. But I can see how useful it is for the user to be able to make a setting to choose a directory of their choice - I will see about making an openomics configuration file at the user directory, located at ~/.openomics/conf.json.

[JonnyTran]

Users can now make the setting openomics.set_cache_dir(path="PATH/OF/YOUR/CHOICE/") which will change the default cache location with https://github.com/BioMeCIS-Lab/OpenOmics/blob/26e2ea4607a3e48f93297abe9f5463ad02c0abe0/openomics/utils/io.py#L18

However, the setting doesn't persist across user sessions. Will implement a ~/.openomics/conf.json settings file later.