🐛: build_combine_archive in utils.py will create multiple manifest.xml files

[luciansmith]

Contact Details

No response

Location

Other (please describe below)

Version

Production (Deployed on a .org domain)

What browsers are you seeing the problem on?

No response

What happened?

If you run build_combine_archive on a directory that already has a manifest.xml file, it will create a new manifest.xml file and add that to the same zip file. This makes it impossible to run on run.biosimulations, since when unzipping the omex file, it asks the user what to do when unpacking two files with the same name, and since it's a batch process, it gets no reply and fails instead. See

https://run.biosimulations.org/runs/63c9a9af3e38811aad1597fc#tab=log

What made it happen?

Run build_combine_archive on a directory containing a manifest.xml file.

Relevant log output

inflating: contents/manifest.xml   
replace contents/manifest.xml? [y]es, [n]o, [A]ll, [N]one, [r]ename:  NULL
(EOF or read error, treating as "[N]one" ...)
srun: error: xanadu-51: task 0: Exited with exit code 1

Code of Conduct

• I agree to follow this project's Code of Conduct