safely execute functions like sci2comm and comm2sci

[sastoudt]

Session Info

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] purrr_0.2.5       taxize_0.9.6      data.table_1.12.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2       xml2_1.2.0       magrittr_1.5     ape_5.3          lattice_0.20-35 
 [6] R6_2.4.0         rlang_0.3.4      foreach_1.4.4    stringr_1.4.0    plyr_1.8.4      
[11] tools_3.5.1      parallel_3.5.1   bold_0.8.6       grid_3.5.1       nlme_3.1-137    
[16] iterators_1.0.10 httpcode_0.2.0   reshape2_1.4.3   codetools_0.2-15 triebeard_0.3.0 
[21] curl_4.0         crul_0.7.4       stringi_1.4.3    compiler_3.5.1   urltools_1.7.2  
[26] jsonlite_1.6     reshape_0.8.8    zoo_1.8-5       

When trying to get scientific names for a vector of common names (or vice versa), one bad request ruins the whole function call.

birdNames = c( "stellers jay" ,    "common raven" ,        "american robin",       "red-tailed hawk" )
test <- comm2sci(unique(birdNames))

No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'stellers jay'

Not found. Consider checking the spelling or alternate classification
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
Error: Bad Request (HTTP 400)

Could the purrr::safely function be wrapped into the function calls to avoid this behavior? Or if you don't want to mess with the core functionality, providing an example of this work around in the documentation could be helpful.

library(purrr)
safe_sciN <- safely(comm2sci)

birdScientific = birdNames %>%  map(safe_sciN)
birdScientificNice = lapply(birdScientific, function(x){x$result[[1]]}) ## grab the result instead of the error, this step could be streamlined with purrr too
birdScientificNice = lapply(birdScientificNice, function(x){ifelse(length(x)==0, NA, x)}) ## add an NA if empty so it keeps the vector size the same, this step could be streamlined with purrr too
birdScientificNice = unlist(birdScientificNice)
birdScientificNice 
## [1] NA                   "Corvus corax"       "Turdus migratorius" "Buteo jamaicensis" 

[sckott]

thanks for this @sastoudt having a look

[sckott]

Those were good suggestions, but i swapped out the stop on nothing found line of code for just returning an empty result. Can you reinstall and try again?

[sastoudt]

Thanks for taking a look so quickly! I re-installed and am getting an error (but a new one):

birdNames = c( "stellers jay" ,    "common raven" ,        "american robin",       "red-tailed hawk" )
test <- comm2sci(unique(birdNames))

No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
══  1 queries  ═══════════════

Retrieving data for taxon 'stellers jay'

Not found. Consider checking the spelling or alternate classification
══  Results  ═════════════════

● Total: 1 
● Found: 0 
● Not Found: 0
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
Error: Bad Request (HTTP 400)

[sckott]

First, it's a good idea to get your own Entrez key. I dont think that's the issue here though.

Did you make sure to restart your R session after installing the new version? Sorry to ask, but many people do not think to do this.

[sastoudt]

Oops, you called it. I did forget to restart my R session. Now it works. Thanks! Can the same fix be made for sci2comm?

[sckott]

great, glad it worked!

i'll have a look at sci2comm