Hello,

I have an error running UniProt.ws R package. It looks like the Uniprot Web Service has been updated but the R package has not been updated accordingly. Is there any plan on updating this package ?

uniprot_object <- UniProt.ws(taxId = 9606)
Error in file(con, "r") : 
  cannot open the connection to 'https://www.uniprot.org/uniprot/?query=organism:9606&format=tab&columns=id'
In addition: Warning message:
In file(con, "r") :
  cannot open URL 'https://rest.uniprot.org/uniprotkb/query=organism:9606&format=tab&columns=id': HTTP status was '400 Bad Request'

sessionInfo( )

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] doParallel_1.0.17   iterators_1.0.14    foreach_1.5.2       RMySQL_0.10.23     
[5] DBI_1.1.3           UniProt.ws_2.36.0   BiocGenerics_0.42.0 RSQLite_2.2.14     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9             lattice_0.20-45        tidyr_1.2.0            GO.db_3.15.0          
 [5] png_0.1-7              Biostrings_2.64.0      assertthat_0.2.1       digest_0.6.29         
 [9] utf8_1.2.2             BiocFileCache_2.4.0    R6_2.5.1               GenomeInfoDb_1.32.2   
[13] stats4_4.2.1           httr_1.4.3             pillar_1.7.0           zlibbioc_1.42.0       
[17] rlang_1.0.3            curl_4.3.2             data.table_1.14.2      SparseM_1.81          
[21] blob_1.2.3             S4Vectors_0.34.0       R.utils_2.12.0         R.oo_1.25.0           
[25] BgeeDB_2.22.3          topGO_2.48.0           RCurl_1.98-1.7         bit_4.0.4             
[29] compiler_4.2.1         pkgconfig_2.0.3        tidyselect_1.1.2       KEGGREST_1.36.2       
[33] tibble_3.1.7           GenomeInfoDbData_1.2.8 codetools_0.2-18       IRanges_2.30.0        
[37] matrixStats_0.62.0     fansi_1.0.3            crayon_1.5.1           dplyr_1.0.9           
[41] dbplyr_2.2.1           bitops_1.0-7           R.methodsS3_1.8.2      rappdirs_0.3.3        
[45] grid_4.2.1             lifecycle_1.0.1        magrittr_2.0.3         graph_1.74.0          
[49] cli_3.3.0              cachem_1.0.6           XVector_0.36.0         ellipsis_0.3.2        
[53] filelock_1.0.2         generics_0.1.3         vctrs_0.4.1            tools_4.2.1           
[57] bit64_4.0.5            Biobase_2.56.0         glue_1.6.2             purrr_0.3.4           
[61] fastmap_1.1.0          AnnotationDbi_1.58.0   BiocManager_1.30.18    memoise_2.0.1

It looks like they completely refactored their rest server to use POST/GET. That's going to require a complete refactor for UniProt.ws as well, which is a bummer. I doubt it will be a quick fix.

I've updated the package to handle these requests on both Bioc devel and release 3.15. Let me know if you have any issues.

Best,

Marcel