wm_attr_data_() Error: (204) No content

[AAlines]

Session Info

Session info ---------------------------------------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.2 (2017-09-28)
 system   i386, mingw32               
 ui       RStudio (1.1.383)           
 language (EN)                        
 collate  English_United Kingdom.1252 
 tz       Europe/London               
 date     2018-08-23                  

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I am trying to get species attribute information using the wm_attr_data_() function for multiple species. However, I am encountering problems when the list of AphiaID's I provide involves an AphiaID of a species with no attribute data at all on the WoRMs page for the particular species.
For example, Here the wm_attr_data_() function works for these 3 species because they all have some attribute data:

library(tidyverse)
library(worrms)
AphiaID <- c(584932, 107381, 126436)
wm_attr_data_(AphiaID, include_inherited = TRUE)

Whereas, when the AphiaID 100373 is added (A species with no attribute data on the WoRMs webpage: http://www.marinespecies.org/aphia.php?p=taxdetails&id=100373) and the following code is used:

AphiaID2 <- c(584932, 107381, 126436, 100373)
wm_attr_data_(AphiaID2, include_inherited = TRUE)

It now returns Error: (204) No Content and does not return any information for the 3 original species.

As I am planning to run this across a much larger set of species. It would perhaps be more useful if it returned the same output as the original example but with a row for the species without attribute information, with NA in each of the attribute fields, so as to avoid the function stopping.

Any advice would be appreciated.
Thanks

[sckott]

thanks @AAlines !

having a look

[hannahmunro]

I think I have a solution using tryCatch(). It needs to be looped using sapply() and cleaned up but it works for me. It is not a perfect solution but might work int he short term.

AphiaID2 <- c(584932, 107381, 126436, 100373)
y<-sapply(AphiaID2,function(i) {tryCatch(wm_attr_data(i), error=function(e) print(i))})
##Cleaning up the list of lists
good<-sapply(y,is.list)
z<-y[good]
all_attributes<-bind_rows(z)

[sckott]

nice one @hannahmunro - I have been working on something, but I had a vacation and conference, so sorry for my slow response @AAlines

[sckott]

@AAlines @hannahmunro try again after reinstalling remotes::install_github("ropensci/worrms@error-vehavior")

(the error-vehavior is not a typo - i spelled it wrong when i created the branch, so we're stuck with that )

[hannahmunro]

@sckott I have tried reinstalling but I am still getting the error.

[sckott]

did you install exactly like remotes::install_github("ropensci/worrms@error-vehavior") and restart your R session?

[hannahmunro]

Works!! I realize now that I didn't restart session, rookie mistake.

I get similar errors when using some of the other functions. Do intend to institute a fix for those other functions too?

[sckott]

can you say which fxn(s)

the way I set it up, the underscore functions have the new behavior as those functions can accept many inputs, but the non-underscore version of the same function name still has the stop on error behavior as it's only meant to deal with 1 input at a time.

[hannahmunro]

I did not realize that you had implemented it for other functions. The ones that I was thinking of have been fixed! Thank you so much for your fix.

[sckott]

great

[sckott]

@AAlines does this work for you now?

[AAlines]

@sckott yes this works for me now.

[sckott]

thanks

[sckott]

done