error accessing KB API through rphenoscape

[meghalithic]

I am working through the paramo tutorial in preparation for the SCATE TraitFest, and am running into the following error:

nex <- lapply(terms, get_ontotrace_data, taxon=taxon, variable_only=TRUE)
Error in get_nexml_data(pkb_api("/ontotrace"), queryseq) : 
  (500) Internal Server Error: There was an internal server error.

May I get help with this?

Note: in the tutorial the argument originally was nex <- lapply(terms, pk_get_ontotrace_xml, taxon=taxon, variable_only=TRUE), but I got this error and changed the argument:

Error in get_nexml_data(pkb_api("/ontotrace"), queryseq) : 
  (500) Internal Server Error: There was an internal server error.
In addition: Warning message:
'FUN' is deprecated.
Use 'get_ontotrace_data' instead.
See help("Deprecated") 

[johnbradley]

@megbalk Are you using the values for "terms" and "taxon" from the PARAMO tutorial? I ran the following without getting the error:

> terms <- c("dermatocranium", "paired fin", "barbel") 
> taxon <- "Siluriformes"  
> nex <- lapply(terms, get_ontotrace_data, taxon=taxon, variable_only=TRUE)
> 

You are correct to replace pk_get_ontotrace_xml with get_ontotrace_data, but that shouldn't be related to your error here. What version of rphenoscape are you using?

[johnbradley]

I believe the error is from the /ontotrace endpoint of the kb phenoscape API server (https://kb.phenoscape.org/api/v2 by default). @balhoff Can you see anything in the logs for that server?

[meghalithic]

I should be using the latest version (I recently installed it, so I assume it pulled the latest)

[balhoff]

@megbalk @johnbradley could you retry now? We had some service restarts here, and the owlery service, which is used by ontotrace, takes a while to start.

[meghalithic]

@balhoff it works! thanks!