Slash characters in investigation title not sanitized for assay file names
mikkonie opened this issue · comments
Describe the Bug
Something originally noticed in SODAR, see bihealth/sodar-server#1896.
If one or more / characters are present in the investigation title, they get carried over to assay file names. This causes an error when Cookiecutter creates a file, as the slash gets intepreted as a path to a folder.
How to Reproduce
Enter a slash character / in the investigation title and try to create the ISA-Tab.
Expected Behavior
We should replace the slash characters with e.g. underscore when forming the assay file name. When entered into the actual investigation file, these characters should be allowed in the investigation title, as AFAIK they are not forbidden by ISA-Tab.
Notes
In Unix/Linux, / should be the only forbidden ASCII character, so we shouldn't have to worry about other special characters.
I noticed this does not actually happen consistently with all templates. For cytof a slash in investigation title works, because it uses the investigation identifier instead of the investigation title for the file name. A slash in the ID does cause the same error however.
For the stem cell core templates this works, as the use the study title and correctly replace the slash characters.
