Cannot load datasets in BioC 3.19 (HTTP 403 error) #23

PeteHaitch · 2024-05-01T05:42:21Z

Not sure if this is a temporary thing and/or related to the in-progress release of BioC 3.19:

suppressPackageStartupMessages(library(celldex))
ImmGenData()
#> Error: SignatureDoesNotMatch (HTTP 403). The request signature we calculated does not match the signature you provided. Check your secret access key and signing method.
MouseRNAseqData()
#> Error: SignatureDoesNotMatch (HTTP 403). The request signature we calculated does not match the signature you provided. Check your secret access key and signing method.
HumanPrimaryCellAtlasData()
#> Error: SignatureDoesNotMatch (HTTP 403). The request signature we calculated does not match the signature you provided. Check your secret access key and signing method.

^{Created on 2024-05-01 with reprex v2.1.0}

Session info

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LTLA · 2024-05-01T06:25:29Z

Hm. I don't have any problems, even when forcibly re-downloading, e.g., with:

se <- fetchReference("immgen", "2024-02-26", realize.assays = TRUE, overwrite=TRUE)

PeteHaitch · 2024-05-01T09:40:39Z

Hmm, it's happening for me locally on home network and when run on a WEHI server.
Also for scRNAseq resources:

scRNAseq::GrunHSCData()
Error: SignatureDoesNotMatch (HTTP 403). The request signature we calculated does not match the signature you provided. Check your secret access key and signing method.

LTLA · 2024-05-01T14:40:00Z

Just tried at work, doesn't happen to me on either Mac or Linux. Dunno what's going on.

You'll have to do some debugging on your end. The relevant function is gypsum::saveVersion. I'm going to guess that the error occurs inside gypsum::listFiles(), probably in the list_objects_v2 call.

PeteHaitch · 2024-05-01T22:02:06Z

I'll see if I can get someone else to reproduce it.
The traceback does show it involves the list_object_v2() call:

#> traceback()
10: stop(error)
9: handler$fn(request)
8: run(request, retry)
7: retry(request)
6: send_request(request)
5: s$list_objects_v2(config$bucket, Prefix = actual.prefix, ContinuationToken = token)
4: listFiles(project, asset, version, config = config)
3: saveVersion(package, name, version, cache = cache, overwrite = overwrite)
2: fetchReference("immgen", "2024-02-26", realize.assays = TRUE)
1: ImmGenData()

at which point:

#> config$bucket
[1] "gypsum-prod"
#> actual.prefix
[1] "celldex/immgen/2024-02-26/"
#> token
NULL

LTLA · 2024-05-02T00:20:37Z

Maybe paws.storage is prioritizing AWS credentials from elsewhere, instead of using that ones supplied by publicS3Config(). This could be diagnosed by running the following:

config0 <- gypsum::publicS3Config()
s <- gypsum:::create_s3(config0)
debug(s$list_objects_v2)
listing <- s$list_objects_v2(config$bucket, Prefix = actual.prefix)

Run down until config is defined inside list_objects_v2, and then have a look at str(config$credentials$creds) and see if they match up with config0.

PeteHaitch · 2024-05-05T22:50:01Z

Not sure I've understood what you're asking for.
But this is what I have and the elements roughly in common between config and config0 seem to match:

# Replicating what happens what I run celldex::ImmGenData()
config <- gypsum::publicS3Config(cache = gypsum:::cacheDirectory())
s <- gypsum:::create_s3(config)
actual.prefix <- "celldex/immgen/2024-02-26/"
token <- NULL
listing <- s$list_objects_v2(config$bucket, Prefix = actual.prefix, 
                             ContinuationToken = token)

# https://github.com/LTLA/celldex/issues/23#issuecomment-2089328586
config0 <- gypsum::publicS3Config()
s <- gypsum:::create_s3(config0)
debug(s$list_objects_v2)
listing <- s$list_objects_v2(config$bucket, Prefix = actual.prefix)

debugging in: s$list_objects_v2(config$bucket, Prefix = actual.prefix)
debug: {
    op <- new_operation(name = "ListObjectsV2", http_method = "GET", 
        http_path = "/{Bucket}?list-type=2", paginator = list(input_token = "ContinuationToken", 
            limit_key = "MaxKeys", output_token = "NextContinuationToken", 
            result_key = list("Contents", "CommonPrefixes")))
    input <- .s3$list_objects_v2_input(Bucket = Bucket, Delimiter = Delimiter, 
        EncodingType = EncodingType, MaxKeys = MaxKeys, Prefix = Prefix, 
        ContinuationToken = ContinuationToken, FetchOwner = FetchOwner, 
        StartAfter = StartAfter, RequestPayer = RequestPayer, 
        ExpectedBucketOwner = ExpectedBucketOwner, OptionalObjectAttributes = OptionalObjectAttributes)
    output <- .s3$list_objects_v2_output()
    config <- get_config()
    svc <- .s3$service(config)
    request <- new_request(svc, op, input, output)
    response <- send_request(request)
    return(response)
}
Browse[1]> 
debug: op <- new_operation(name = "ListObjectsV2", http_method = "GET", 
    http_path = "/{Bucket}?list-type=2", paginator = list(input_token = "ContinuationToken", 
        limit_key = "MaxKeys", output_token = "NextContinuationToken", 
        result_key = list("Contents", "CommonPrefixes")))
Browse[1]> 
debug: input <- .s3$list_objects_v2_input(Bucket = Bucket, Delimiter = Delimiter, 
    EncodingType = EncodingType, MaxKeys = MaxKeys, Prefix = Prefix, 
    ContinuationToken = ContinuationToken, FetchOwner = FetchOwner, 
    StartAfter = StartAfter, RequestPayer = RequestPayer, ExpectedBucketOwner = ExpectedBucketOwner, 
    OptionalObjectAttributes = OptionalObjectAttributes)
Browse[1]> 
debug: output <- .s3$list_objects_v2_output()
Browse[1]> 
debug: config <- get_config()
Browse[1]> 
debug: svc <- .s3$service(config)

Browse[1]> names(config$credentials$creds)
[1] "access_key_id"     "secret_access_key" "session_token"     "access_token"      "expiration"        "provider_name"    
Browse[1]> names(config0)
[1] "endpoint" "bucket"   "key"      "secret" 
Browse[1]> identical(as.character(config$credentials$creds$access_key_id), config0$key)
[1] TRUE
Browse[1]> identical(as.character(config$credentials$creds$secret_access_key), config0$secret)
[1] TRUE

I can't find any other AWS credentials on any of the 2 laptops and 1 server where I'm having problems with this.

LTLA · 2024-05-07T15:49:21Z

Well, I dunno what's going on with the S3 API. So I just modified gypsum to download files and such via HTTP instead. Try installing the latest master at https://github.com/ArtifactDB/gypsum-R and it should fix the problem.

LTLA · 2024-05-07T17:02:53Z

FWIW my new suspicion is that auto is not resolving correctly. Perhaps try

config <- gypsum::publicS3Config()

s <- paws.storage::s3(
    endpoint=config$endpoint,
    region="us-east-1", # swapped with "auto"
    credentials=list(
        creds=list(
            access_key_id=config$key,
            secret_access_key=config$secret
        )
    )
)

s$list_objects_v2(config$bucket, Delimiter="/")

With and without "auto" in the region, and see if it changes anything.

PeteHaitch · 2024-05-08T00:27:30Z

No difference apart from the obvious in specifying the region:

config <- gypsum::publicS3Config()

s1 <- paws.storage::s3(
  endpoint=config$endpoint,
  region="us-east-1", # swapped with "auto"
  credentials=list(
    creds=list(
      access_key_id=config$key,
      secret_access_key=config$secret
    )
  )
)

s1$list_objects_v2(config$bucket, Delimiter="/")
#> $IsTruncated
#> [1] FALSE
#> 
#> $Contents
#> list()
#> 
#> $Name
#> [1] "gypsum-prod"
#> 
#> $Prefix
#> character(0)
#> 
#> $Delimiter
#> [1] "/"
#> 
#> $MaxKeys
#> [1] 1000
#> 
#> $CommonPrefixes
#> $CommonPrefixes[[1]]
#> $CommonPrefixes[[1]]$Prefix
#> [1] "..logs/"
#> 
#> 
#> $CommonPrefixes[[2]]
#> $CommonPrefixes[[2]]$Prefix
#> [1] "celldex/"
#> 
#> 
#> $CommonPrefixes[[3]]
#> $CommonPrefixes[[3]]$Prefix
#> [1] "scRNAseq/"
#> 
#> 
#> $CommonPrefixes[[4]]
#> $CommonPrefixes[[4]]$Prefix
#> [1] "test-R-perms/"
#> 
#> 
#> $CommonPrefixes[[5]]
#> $CommonPrefixes[[5]]$Prefix
#> [1] "test-R-quota/"
#> 
#> 
#> $CommonPrefixes[[6]]
#> $CommonPrefixes[[6]]$Prefix
#> [1] "test-R/"
#> 
#> 
#> 
#> $EncodingType
#> character(0)
#> 
#> $KeyCount
#> [1] 6
#> 
#> $ContinuationToken
#> character(0)
#> 
#> $NextContinuationToken
#> character(0)
#> 
#> $StartAfter
#> character(0)
#> 
#> $RequestCharged
#> character(0)


s2 <- paws.storage::s3(
  endpoint=config$endpoint,
  # region="us-east-1", # swapped with "auto"
  region="auto", # swapped with "auto"
  credentials=list(
    creds=list(
      access_key_id=config$key,
      secret_access_key=config$secret
    )
  )
)

s2$list_objects_v2(config$bucket, Delimiter="/")
#> $IsTruncated
#> [1] FALSE
#> 
#> $Contents
#> list()
#> 
#> $Name
#> [1] "gypsum-prod"
#> 
#> $Prefix
#> character(0)
#> 
#> $Delimiter
#> [1] "/"
#> 
#> $MaxKeys
#> [1] 1000
#> 
#> $CommonPrefixes
#> $CommonPrefixes[[1]]
#> $CommonPrefixes[[1]]$Prefix
#> [1] "..logs/"
#> 
#> 
#> $CommonPrefixes[[2]]
#> $CommonPrefixes[[2]]$Prefix
#> [1] "celldex/"
#> 
#> 
#> $CommonPrefixes[[3]]
#> $CommonPrefixes[[3]]$Prefix
#> [1] "scRNAseq/"
#> 
#> 
#> $CommonPrefixes[[4]]
#> $CommonPrefixes[[4]]$Prefix
#> [1] "test-R-perms/"
#> 
#> 
#> $CommonPrefixes[[5]]
#> $CommonPrefixes[[5]]$Prefix
#> [1] "test-R-quota/"
#> 
#> 
#> $CommonPrefixes[[6]]
#> $CommonPrefixes[[6]]$Prefix
#> [1] "test-R/"
#> 
#> 
#> 
#> $EncodingType
#> character(0)
#> 
#> $KeyCount
#> [1] 6
#> 
#> $ContinuationToken
#> character(0)
#> 
#> $NextContinuationToken
#> character(0)
#> 
#> $StartAfter
#> character(0)
#> 
#> $RequestCharged
#> character(0)

all.equal(s1, s2)
#> [1] "Component \".internal\": Component \"config\": Component \"region\": 1 string mismatch"

Session info

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#>  rmarkdown      2.26    2024-03-05 [1] CRAN (R 4.4.0)
#>  rstudioapi     0.16.0  2024-03-24 [1] CRAN (R 4.4.0)
#>  sessioninfo    1.2.2   2021-12-06 [1] CRAN (R 4.4.0)
#>  withr          3.0.0   2024-01-16 [1] CRAN (R 4.4.0)
#>  xfun           0.43    2024-03-25 [1] CRAN (R 4.4.0)
#>  xml2           1.3.6   2023-12-04 [1] CRAN (R 4.4.0)
#>  yaml           2.3.8   2023-12-11 [1] CRAN (R 4.4.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

But using current master at https://github.com/ArtifactDB/gypsum-R does work!
Thank you for fixing this for me.

This was referenced May 7, 2024

Cannot load dataset #24

Open

Use REST endpoints for downloading files, listing bucket contents. ArtifactDB/gypsum-R#6

Merged

LTLA closed this as completed in ArtifactDB/gypsum-R#6 May 7, 2024

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Cannot load datasets in BioC 3.19 (HTTP 403 error) #23

Cannot load datasets in BioC 3.19 (HTTP 403 error) #23

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Cannot load datasets in BioC 3.19 (HTTP 403 error) #23

Cannot load datasets in BioC 3.19 (HTTP 403 error) #23

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