Hello,

I am trying to figure out if it is possible to use STRINGdb offline, assuming that all the necessary files have been downloaded locally. I am running

library(STRINGdb)
strdb <- STRINGdb$new(version = "11.5", species = 10090, 
                      score_threshold = 400, input_directory = "~/Desktop/stringdb")
print(strdb) ## this triggers the download of files from STRING to the local directory
strdb$map(data.frame(x = "Sox2"), "x", removeUnmappedRows = FALSE)  ## this downloads the alias file and maps the ID

which will download the necessary files. If I then re-execute the mapping or the initialization of the strdb object, the files will not be re-downloaded. So far, so good.

Now, if I disconnect from the internet and try to re-initialize the object, I get an error as R is not able to open the connection to https://string-db.org/api/tsv-no-header/version:

Error in open.connection(file, "rt") : 
  cannot open the connection to 'https://string-db.org/api/tsv-no-header/version'
In addition: Warning message:
In open.connection(file, "rt") :
  URL 'https://string-db.org/api/tsv-no-header/version': Timeout of 60 seconds was reached

Is there any way that I can force STRINGdb to use the local files, without checking in with the remote server?

Thanks!

Session info:

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] STRINGdb_2.10.1

loaded via a namespace (and not attached):
 [1] igraph_1.4.1       hash_2.2.6.2       Rcpp_1.0.10        rstudioapi_0.14    magrittr_2.0.3    
 [6] bit_4.0.5          rlang_1.0.6        fastmap_1.1.1      blob_1.2.3         plyr_1.8.8        
[11] caTools_1.18.2     tools_4.2.2        png_0.1-8          plotrix_3.8-2      KernSmooth_2.23-20
[16] cli_3.6.0          DBI_1.1.3          gtools_3.9.4       bit64_4.0.5        RColorBrewer_1.1-3
[21] vctrs_0.5.2        bitops_1.0-7       RCurl_1.98-1.10    cachem_1.0.7       memoise_2.0.1     
[26] RSQLite_2.3.0      gsubfn_0.7         compiler_4.2.2     gplots_3.1.3       chron_2.3-59      
[31] sqldf_0.4-11       proto_1.0.0        pkgconfig_2.0.3

Unfortunately, it's not possible. Some features can't work without access to STRING's API, like generating the image, payload, and enrichment functionality. In the future update, the mapping will also move to the API. This is all done for the sake of consistency, so any improvements to STRING's algorithms (between the versions) will be applicable to the STRINGdb package as well. It's impossible for us to maintain the two code bases in sync.

If you do not use images, payload, or the enrichment and only the network, in principle we can skip the version check, and AFAIK it should work. That said you are then better off simply using the STRING package once for mapping and then loading the network from the flat files (found in the download section of STRING, which is where the package gets it from), and do not bother with the package anymore, as it doesn't really give you a lot of additional functionality.

Hope it's clearer, why the package needs access.

Thanks for the feedback!

Damian.