Dead URLs in DefaultCWLCreator

[eladrion]

The file contains URLs to https://raw.githubusercontent.com/Workflomics/DemoKit/... which does not exist, see this line, for example.

[eladrion]

@vedran-kasalica What should I do here?

[vedran-kasalica]

As I can see they are valid URLs, however the implementation is far from perfect. We used those as demo examples. If APE detects the corresponding data type as input, it would inject these values to inputs.yaml file so the user can run the workflows without having to provide the data even. However, this is an extremely fragile system. I would suggest having these as part of the domain annotation, and per domain the domain expert could provide few demo files (especially the files needed to run the default/demo configuration).

[eladrion]

Hi @vedran-kasalica, at least goa_human_smaller.gaf does not exist in DemoKit. And also, I was more referring to the EDAM urls (e.g. http://edamontology.org/format_3475_plain) and it seems to be the plain variant which is dead.

[vedran-kasalica]

I guess that there was a mistake there then, the link should have been https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/goa_human.gaf (without _smaller).

On the other hand, suffix _plain is an APE construct, used to enforce subsumption relation to be complete. For example, JSON_plain would be a basic/plain subset of the class JSON. It would contain all the instances (files) that are JSON and do not belong to other (more specialised) JSON subclasses. In your example http://edamontology.org/format_3475 is a TSV file, so by using http://edamontology.org/format_3475_plain I made sure to only suggest the reference TSV file, if the input file type is not expected to be MAGE-TAB, RPKM nor WEGO.

[eladrion]

Okay @vedran-kasalica , then I will only fix the reference to goa_human.gaf. Is the subsumption (plain) documented somewhere? I would at least also add a comment about that in the code.