How to handle using API token

[inodb]

cBioPortal provides a way to connect to authenticated portals using an API token. I'm guessing we can pass the token to rapiclient somehow. This probably isn't too tricky. Volunteering myself to solve this

[LiNk-NY]

@inodb Do you have an example? The AnVIL::Service class allows for authentication. Perhaps that is enough?

[inodb]

@LiNk-NY not directly an example but could try that, thanks for the suggestion!

The docs are here:

https://docs.cbioportal.org/2.2-authorization-and-authentication/authenticating-users-via-tokens#using-data-access-tokens

need to have some way to add an authorization header to each request like:

curl \
     -X GET "http://www.cbioportal.org/api/studies" \
     -H "accept: application/json" \
     -H "Authorization: Bearer 63efa81c-2490-4e15-9d1c-fb6e8e50e35d"

[LiNk-NY]

Yup, it looks like the Service class supports it.

[LiNk-NY]

@inodb I would look at the AnVIL package for some examples using authentication

[schaffman5]

I ran into this issue as well and there is a larger issue with the rapiclient package as I reported here https://github.com/bergant/rapiclient/issues/18. One workaround is to manually create the service, but this uses non-public methods. Perhaps there is a more elegant way to fix this or rely less on the rapiclient for this functionality.

# override get_api function in rapiclient R package
my_get_api <- function (url, config = NULL){
  api = NULL
  api <- tryCatch({
    # new code to properly handle the config parameters instead of just
    # calling jsonlite::fromJSON directly with the url and no other parameters
    res<-httr::GET(url, type="text/json", config=config)
    res.json<-httr::content(res, as="text", encoding="UTF-8")
    jsonlite::fromJSON(res.json, simplifyDataFrame = FALSE)
    # end of new code

    # old code:
    # jsonlite::fromJSON(url, simplifyDataFrame = FALSE)
  }, error = function(x) NULL)
  if (is.null(api))
    tryCatch({
      if (startsWith(url, "http")) {
        url0 <- url(url)
        open(url0)
        api <- yaml::yaml.load_file(url0) # this probably also needs to handle config
        close(url0)
      }
      else {
        api <- yaml::yaml.load_file(url)
      }
    }, error = function(x) NULL)
  if (is.null(api))
    stop("'url' does not appear to be JSON or YAML")
  if (is.null(api$swagger)) {
    warning("Missing Swagger Specification version")
  }
  if (is.null(api$info)) {
    warning("Missing Specification Info")
  }
  if (is.null(api$host)) {
    host <- httr::parse_url(url)$hostname
    if (!is.null(host)) {
      port <- httr::parse_url(url)$port
      if (!is.null(port)) {
        host <- paste0(host, ":", port)
      }
      api$host <- host
    }
  }
  if (is.null(api$basePath)) {
    api$basePath <- ""
  }
  api$basePath <- gsub("/$", "", api$basePath)
  if (is.null(api$schemes)) {
    api$schemes <- httr::parse_url(url)$scheme
  }
  if (is.null(api$paths)) {
    warning("There is no paths element in the API specification")
  }
  if (!(is.null(config) || inherits(config, "request")))
    stop("'config' must be NULL or an instance of httr::config()")
  api$config <- config
  class(api) <- c(rapiclient:::.class_api, class(api)) # added rapiclient:::.class_api
  api
}

Then the following will work.

cbio.api.url<-"<your_cbio_url>/api/api-docs"
cbio.token<-"<your_cbio_token>"

config <- httr::add_headers(Authorization = sprintf("Bearer %s", cbio.token))

cbio.api<-my_get_api(cbio.api.url, config)

cbioService<-AnVIL:::.Service(service ="cBioPortal", config=config, api = cbio.api)
cbio<-cBioPortalData:::.cBioPortal(cbioService)

cBioPortalData::getStudies(cbio)
cBioPortalData::clinicalData(cbio, "acc_tcga")

[LiNk-NY]

Hi @schaffman5

This is related to https://github.com/Bioconductor/AnVIL/issues/42 I've created a branch called token in cBioPortalData based on the changes in the AnVIL branch.

You can test this functionality with:

devtools::install_github("waldronlab/cBioPortalData", ref = "token")
devtools::install_github("Bioconductor/AnVIL", ref = "Service_api_header")

Let me know if this works. Best, Marcel

[schaffman5]

Thanks. The cBioPortalData branch you referenced requires R version 4.2.0, which is not a current release. Could you modify the Description file to allow v4.1.0 instead?

[LiNk-NY]

Hi @schaffman5

The proposed changes would get merged to the Bioc-devel branch which currently uses R-devel. The R >= 4.2.0 is appropriate. For testing, you could modify the R version on a local checkout.

Best, Marcel

[schaffman5]

@LiNk-NY Yes, the token branch works on our internal cBioPortal deployment. Thanks!

[LiNk-NY]

This should be implemented. Feel free to comment if you have any further issues with API tokens.

[ZWael]

Hi @schaffman5

The proposed changes would get merged to the Bioc-devel branch which currently uses R-devel. The R >= 4.2.0 is appropriate. For testing, you could modify the R version on a local checkout.

Best, Marcel

Hi I'am using R version 4.1 and i have installed CbioPortalData from bioconductor which install the version 2.6.1 but unfortunately it is not yet supporting token argument in the cBioPortal() function using devtools::install_github("waldronlab/cBioPortalData", ref = "token") require R 4.2 how can i make it work in R 4.1?

[LiNk-NY]

This feature is not available in R < 4.2. It is only available in Bioconductor-devel or soon-to-be RELEASE_3_15 .