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Merged
Gautam8387 merged 4 commits into from
Aug 10, 2026
Merged

Add browser authentication and cytetyper CLI support #54

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ca2a3a2
Add browser authentication and cytetyper CLI support
Gautam8387 Aug 9, 2026
f56695d
bug fix
Gautam8387 Aug 9, 2026
1ee55f1
fix tests
Gautam8387 Aug 10, 2026
598bcbc
cli setup check
Gautam8387 Aug 10, 2026
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7 changes: 5 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,24 +1,26 @@
Package: CyteTypeR
Title: CyteType for R
Version: 0.4.2
Version: 0.4.3
Description: CyteTypeR is the R version of CyteType python package.
Authors@R:
person("Nygen Analytics AB", , ,"contact@nygen.io", role = c("aut", "cre"))
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends:
R (>= 4.1.0)
Imports:
askpass,
cli,
crayon,
dplyr,
httpuv,
httr2,
jsonlite,
logger,
Matrix,
methods,
openssl,
purrr,
rhdf5,
Seurat,
Expand All @@ -37,3 +39,4 @@ Remotes:
bioc::rhdf5
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
6 changes: 6 additions & 0 deletions NAMESPACE
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Expand Up @@ -4,7 +4,13 @@ S3method(print,cytetype_api_error)
export(CleanUpArtifacts)
export(CyteTypeR)
export(GetResults)
export(InstallCyteTypeRCli)
export(LoginCyteTypeR)
export(LogoutCyteTypeR)
export(OpenCyteTypeDashboard)
export(PrepareCyteTypeR)
export(SetupCyteTypeR)
export(ViewCyteTypeJob)
export(cytetype_api_error)
importFrom(Matrix,rowSums)
importFrom(Seurat,AddMetaData)
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14 changes: 11 additions & 3 deletions R/api.R
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Expand Up @@ -39,7 +39,9 @@
req <- req |> req_auth_bearer_token(auth_token)
}

response <- req |> req_perform()
response <- req |>
httr2::req_error(is_error = function(resp) resp_status(resp) == 429L) |>
req_perform()
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status_code <- resp_status(response)

# Handle specific status codes with switch for clarity
Expand All @@ -49,11 +51,17 @@
},
"401" = {
log_debug("Authentication failed for job {job_id}")
stop("Authentication failed: Invalid or expired auth token")
.stop_authentication(
"Authentication failed: Invalid or expired auth token",
"INVALID_TOKEN"
)
},
"403" = {
log_debug("Authorization failed for job {job_id}")
stop("Authorization failed: Access denied")
.stop_authentication(
"Authorization failed: Access denied",
"ACCESS_DENIED"
)
}
)

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