Shims/transforms for biotoolsSchema-compatibale metadata : advice needed!

[joncison]

Chaps (@hansioan @hmenager @matuskalas @bgruening @albangaignard) - please help.

I want to get the biotoolsSchema paper out of the door and the main outstanding thing is elegant handling of the serialisation formats:  
-  biotoolsSchema-compliant XML, JSON and YAML formats 
-  shims for interconverting these
-  validation against biotoolsSchema / biotoolsSchemaJ

... all of this also useful for ETP "ecosystem".

Until now (for purposes of XML support in bio.tools) I'd created shims as XSLT transforms, which worked fine.  But this gets unmanageable for any-to-any interconversion  of XML, JSON and YAML - especially as we might need JSON-LD, and perhaps other formats in future (codemeta, whatever).

So I figure the elegant solution is to write a single utility in python (biotoolsshim.py) for all our tool metadata shimming/transformation needs.  Now, from my newbie-python perspective this isn't looking too hard BUT a spanner in the works is the <Summary> and <Labels> elements in the XSD - these complicate what (I think) would otherwise be a fairly straightforward exercise.  I could program around it, but it seems daft to do so!

<Summary> and <Labels>  are purely "organisational" (do not appear in biotoolsSchemaJ as documented here), so I'm thinking to release biotoolsSchema 3.3.0 which drops these elements, paving the way for easier coding. 

PS. The XSD I think has mostly served its purpose, and expect in future to focus on the JSON schema variant (biotoolsSchemaJ).  

I'm writing to get your input on this - any thoughts or suggestions much appreciated!

Thanks a million  

[joncison]

Hi @hansioan cc @hmenager

biotoolsSchema 3.3.0 is now out and along with it the shims for format handling / serialisation in bio.tools:

• xml2genericxml
• xml2genericxml-singletool
• genericxml2xml
• genericxml2xml-singletool

I haven't triple-checked everything (will do tomorrow) but it's ready for testing.

Cheers!

PS. in future I think the focus should be on biotoolsSchemaJ + a utility for general-purpose file reformatting.