fix: add authorization grant refreshing token

[clemens-tolboom]

No description provided.

[timcadman]

This fails after 15 mins with the message:

! There are some DataSHIELD errors, list them with datashield.errors()
Run `rlang::last_trace()` to see where the error occurred.
> datashield.errors()
$study1
[1] "Unauthorized"

To reproduce:

library(dsBaseClient)
library(purrr)

demo_url <- "https://armadillo-demo.molgenis.net/"
demo_token <- armadillo.get_token(demo_url)

builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1", url = demo_url, profile = "xenon", token = demo_token, driver = "ArmadilloDriver", 
               table = "xenon-tests/2_1-core-1_0/nonrep")
logindata <- builder$build()

conns <- DSI::datashield.login(logins = logindata, assign = T, symbol = "nonrep")

1:100000 %>% map(
  ~ds.rep(x1 = 4, times = 6, length.out = NA, each = 1, source.x1 = "clientside",
          source.times = "c", source.length.out = NULL, source.each = "c",
          x1.includes.characters = FALSE, newobj = "rep.seq"))

[clemens-tolboom]

Error in `map()`:
ℹ In index: 3452.
Caused by error:
! There are some DataSHIELD errors, list them with datashield.errors()
Run `rlang::last_trace()` to see where the error occurred.

> rlang::last_trace()
<error/purrr_error_indexed>
Error in `map()`:
ℹ In index: 1.
Caused by error:
! There are some DataSHIELD errors, list them with datashield.errors()
---
Backtrace:
     ▆
  1. ├─1:1e+05 %>% ...
  2. └─purrr::map(...)
  3.   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  4.     ├─purrr:::with_indexed_errors(...)
  5.     │ └─base::withCallingHandlers(...)
  6.     ├─purrr:::call_with_cleanup(...)
  7.     └─.f(.x[[i]], ...)
  8.       └─dsBaseClient::ds.rep(...)
  9.         └─DSI::datashield.assign(datasources, newobj, calltext)
 10.           └─DSI::datashield.assign.expr(...)
 11.             └─DSI:::.checkLastErrors()
 12.               └─base::stop(...)
Run rlang::last_trace(drop = FALSE) to see 4 hidden frames.

> rlang::last_trace(drop = FALSE)
<error/purrr_error_indexed>
Error in `map()`:
ℹ In index: 1.
Caused by error:
! There are some DataSHIELD errors, list them with datashield.errors()
---
Backtrace:
     ▆
  1. ├─1:1e+05 %>% ...
  2. ├─purrr::map(...)
  3. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  4. │   ├─purrr:::with_indexed_errors(...)
  5. │   │ └─base::withCallingHandlers(...)
  6. │   ├─purrr:::call_with_cleanup(...)
  7. │   └─.f(.x[[i]], ...)
  8. │     └─dsBaseClient::ds.rep(...)
  9. │       └─DSI::datashield.assign(datasources, newobj, calltext)
 10. │         └─DSI::datashield.assign.expr(...)
 11. │           └─DSI:::.checkLastErrors()
 12. │             └─base::stop(...)
 13. └─base::.handleSimpleError(...)
 14.   └─purrr (local) h(simpleError(msg, call))
 15.     └─cli::cli_abort(...)
 16.       └─rlang::abort(...)

[clemens-tolboom]

1:100000 %>% map(
  ~{
    Sys.sleep(10)
    print(.)
    print(format(Sys.time(), "%Y-%m-%dT%H:%M:%S"))
    ds.rep(x1 = 4, times = 6, length.out = NA, each = 1, source.x1 = "clientside",
          source.times = "c", source.length.out = NULL, source.each = "c",
          x1.includes.characters = FALSE, newobj = "rep.seq")
  })

running again

[1] 1
[1] "2024-03-13T10:01:47"
  Assigned expr. (rep.seq <- repDS(x1.transmit = "4", times.transmit = "6", length.out.transmit =...
  Aggregated (testObjExistsDS("rep.seq")) [==============================================] 100% / 0s
  Aggregated (messageDS("rep.seq")) [====================================================] 100% / 0s

...

[1] 93
[1] "2024-03-13T10:17:40"
  Assigned expr. (rep.seq <- repDS(x1.transmit = "4", times.transmit = "6", length.out.transmit =...Error in `map()`:
ℹ In index: 93.
Caused by error:
! There are some DataSHIELD errors, list them with datashield.errors()
Run `rlang::last_trace()` to see where the error occurred.

17:40 - 1:47 = 15:53 ... so our timeout of 15 minutes checks

[clemens-tolboom]

After some puzzling got this running on DEV

#!/usr/bin/env Rscript

library(dsBaseClient)
library(purrr)

#demo_url <- "https://armadillo-demo.molgenis.net/"
demo_url <- "http://localhost:8080/"
demo_token <- armadillo.get_token(demo_url)

builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1", url = demo_url, profile = "default", token = demo_token, driver = "ArmadilloDriver", 
               table = "lifecycle/core/nonrep")
logindata <- builder$build()

conns <- DSI::datashield.login(logins = logindata, assign = T, symbol = "nonrep")

1:100000 %>% map(
  ~{
    Sys.sleep(10)
    print(.)
    print(format(Sys.time(), "%Y-%m-%dT%H:%M:%S"))
    ds.rep(x1 = 4, times = 6, length.out = NA, each = 1, source.x1 = "clientside",
          source.times = "c", source.length.out = NULL, source.each = "c",
          x1.includes.characters = FALSE, newobj = "rep.seq")
  })

[clemens-tolboom]

grep -i auth.molgenis.org logs/armadillo.log

gives

2024-03-13 11:06:29.622 [main|] DEBUG o.s.web.client.RestTemplate - HTTP GET https://oidc-provider/.well-known/openid-configuration

...

2024-03-13 11:11:45.077 [http-nio-8080-exec-10|] DEBUG o.s.web.client.RestTemplate - HTTP GET https://oidc-provider/.well-known/jwks.json
...

Guess that's a config poll for changes on the OIDC provider.

[clemens-tolboom]

Test did not succeed as using different OICD does not help while testing.

[mswertz]

we believe it is better to stop 'molgenisAuth.r' and instead use htt2 in both molgenis-r-armadillo and molgenis-r-datashield.

httr2 has device workflow and refresh token capabilities.

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarCloud

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud