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sbg / sevenbridges-r

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R
https://sbg.github.io/sevenbridges-r/
Apache License 2.0
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baseCommand is empty after convert_app() #59

Closed tdelhomme closed 7 years ago

tdelhomme commented 7 years ago

When I try to convert a public app to a tool, the base command is lost.

> t=convert_app(a$public_app(name = "bgzip"))
Warning message:
In .asTool(obj) :
  Extra fields dropped before conversion: sbg:appVersion sbg:projectName cwlVersion

> t$baseCommand
NULL
tdelhomme commented 7 years ago

@tengfei I have the same problem when trying to convert an app from JSON file following the tutorial here... 

> t1 = system.file("extdata/app", "tool_star.json", package = "sevenbridges")
> # # convert json file into a Tool object
> t1 = convert_app(t1)
> t1$baseCommand
NULL

weird!

tdelhomme commented 7 years ago

It seems that it happens only when use an array for baseCommand in JSON file, if string is used, baseCommand is well imported in R.

tengfei commented 7 years ago

Thanks @tdelhomme, it's good catch, I just fix the bug and push it on github with recent two commits. (I also fix warning you got). Please let me know if it still doesn't work

nanxstats commented 7 years ago

-great! Thanks @tengfei for the fix. I've just pushed the latest changes to Bioconductor. The new version (release: 1.6.4, devel: 1.7.4) will propagate through Bioc's build system and appear on their website in about 24 hours.