ropensci/rcrossref

cr_works returning error when querying some DOIs

nicholasmfraser opened this issue · 3 comments

nicholasmfraser commented

I've encountered instances of the cr_works route failing on a very small number of DOIs, for example:

cr_works(doi="10.3389/fgene.2017.00147")

returns

Error in w[sapply(w, function(b) length(b) == 0)] <- NULL : 
  invalid subscript type 'list'

I think the problem lies in the parse_todf function in cr_works.R. When Crossref returns an empty list (in the case of the DOI record referenced above, under funder[1], see API response) the parse function fails. For now I'm using the cr_works_ low level route instead, which works fine.

Changing lines 349-350 from:

w[sapply(w, function(b) length(b) == 0)] <- NULL
data.frame(w, stringsAsFactors = FALSE)`

to

if(length(w) > 0) {
    w[sapply(w, function(b) length(b) == 0)] <- NULL
    data.frame(w, stringsAsFactors = FALSE)
}

seems to work, but I haven't tested extensively.

Session Info 
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] rcrossref_0.8.4 forcats_0.3.0   stringr_1.3.1   dplyr_0.7.6     purrr_0.2.5     readr_1.1.1     tidyr_0.8.1    
 [8] tibble_1.4.2    ggplot2_3.0.0   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.4 haven_1.1.2      lattice_0.20-35  colorspace_1.3-2 miniUI_0.1.1.1   htmltools_0.3.6  yaml_2.2.0      
 [8] utf8_1.1.4       rlang_0.3.0.1    pillar_1.3.0     later_0.7.3      httpcode_0.2.0   glue_1.3.0       withr_2.1.2     
[15] modelr_0.1.2     readxl_1.1.0     bindrcpp_0.2.2   bindr_0.1.1      plyr_1.8.4       munsell_0.5.0    gtable_0.2.0    
[22] cellranger_1.1.0 rvest_0.3.2      htmlwidgets_1.2  knitr_1.20       httpuv_1.4.5     curl_3.2         fansi_0.2.3     
[29] triebeard_0.3.0  urltools_1.7.1   broom_0.5.0      Rcpp_0.12.18     xtable_1.8-2     DT_0.4           scales_1.0.0    
[36] backports_1.1.2  promises_1.0.1   jsonlite_1.5     mime_0.5         hms_0.4.2        digest_0.6.15    stringi_1.1.7   
[43] shiny_1.1.0      bibtex_0.4.2     grid_3.5.1       cli_1.0.0        tools_3.5.1      magrittr_1.5     lazyeval_0.2.1  
[50] crul_0.6.0       crayon_1.3.4     pkgconfig_2.0.1  xml2_1.2.0       lubridate_1.7.4  assertthat_0.2.0 httr_1.3.1      
[57] rstudioapi_0.7   R6_2.2.2         nlme_3.1-137     compiler_3.5.1
sckott commented

thanks for the report @nicholasmfraser

i can replicate the issue. ill see about that change

sckott commented

@nicholasmfraser reinstall and try again, shoud be fixed now

nicholasmfraser commented

@sckott works fine now, thanks for the quick fix!

  • 👍1