Issue when using DSI::datashield.assign.resource

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1

Hi, I am trying to upload a rds file as resource into a DataSHIELD project in order to perform DGE analysis on it. (All of the following was run as system administrator). I tried using the airway pre-defined R object (RangedSummarizedExperiment). On dataSHIELD, I created a project named AIRWAY and then uploaded the file with:

saveRDS(airway, "airway.rds")
opal.file_upload(o, "./airway.rds", "/projects/AIRWAY")
opal.resource_create(o, "AIRWAY", "airway", url = "opal+https://127.0.0.1:443/ws/files/projects/AIRWAY/airway.rds")
opal.resource_perm_add(o, "AIRWAY", "airway", subject = “administrator”, type = "user", permission = "view")

However when trying to retrieve and use this object in R using

builder <- newDSLoginBuilder()
builder$append(server = "server1",  url = "https://127.0.0.1:443",
               user = "administrator", password = “P@ssw0rd”, 
               driver = "OpalDriver", 
               options='list(ssl_verifyhost=0, ssl_verifypeer=0)')

logindata <- builder$build()
conns <- datashield.login(logins = logindata, assign = TRUE, symbol = "res")
datashield.resources(conns)
datashield.assign.resource(conns, "rse", "RSRC.prova")
datashield.assign.expr(conns, "res", quote(as.resource.object(rse, strict = TRUE)))

I get

datashield.errors()
✖ server1: Command 'org.obiba.opal.web.datashield.DataShieldSymbolResourceImpl$DataShieldROperation@79ab4556'
  failed on 'server1': Error while evaluating 'is.null(base::assign('rse',
  resourcer::newResourceClient(resourcer::newResource(name='airway.rds',
  url='opal+https://127.0.0.1:443/ws/files/projects/AIRWAY/airway.rds', identity=NULL, secret=NULL,
  format=NULL))))' -> Error in resolveResource(x) : No resolver could be found for resource:
  opal+https://127.0.0.1:443/ws/files/projects/AIRWAY/airway.rds

Is this the correct procedure to upload and use an rds file as resource into DataSHIELD? If not, can you please indicate the correct way of doing so?

Francesco

2

Hi,

Your resource is a file to be downloaded from Opal. You did not specify a secret in your resource definition, which in the case of Opal is expected to be a Personal Access Token (PAT). Then Opal refuses that the R server downloads this file.

See opal.resource_create documentation, there is an example:

Regards
Yannick