Failed getting biosample with ID 311754778: BASESPACE.COMMON.NOT_FOUND: Resource not found at the given path

[Ross]

Hello,

"Failed getting biosample with ID 311754778: BASESPACE.COMMON.NOT_FOUND: Resource not found at the given path"

I get the above error when I try to launch a basespace app as follows:

bs launch application -i 9192183 -o database:https://use1-prd-seq-hub-appdata.s3.amazonaws.com/16S_Metagenomics_v1.1/RefSeq-RDP16S_v3_May2018_DADA2_32bp.dat  -o project-id:143655512 -o sample-id:311754778

I have obtained the sample-id from the URL in basespace:

https://basespace.illumina.com/sample/311754778/BS1-FUR86

Using the same CLI settings, I have managed to download the sample using it's name BS1-FUR86 but not using it's ID. Am I not using the correct ID? The app I'm calling doesn't take name so I can't use that.

Any ideas why it's not finding the sample using it's ID as per the URL?

thank you

[Nick Vinckier]

Hi Ross,

From the look of that URL this might be a Classic Sample ID (from an older version of the BaseSpace API), whereas the app may be expecting it's BioSample ID (which is different and part of the New BaseSpace API). You can either switch your BaseSpace Application version (in Settings) to New and get the BioSample ID from the URL when on the BioSample page for BS1-FUR86. Or, and perhaps more helpful, you can list your biosamples and either grep for that BioSample, or use the BaseSpace CLI --filter-term and --filter-field. Or, you can narrow the list of BioSamples returned by limiting to a specific project ID with the --project-id.

Hopefully that helps, if you're still hitting issues, I might suggest emailing techs...@illumina.com if you've not already done so.

Cheers,

Nick

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[Ross]

Hi Nick,

thank you, that helped and I managed to get it working once I found the correct biosample ID.

I wonder if you can help with another question? This time it's specific to an illumina application (9192183)

Can you possibly help me translate this CLI command to it's rest API (v1)  json equivalent?

bs launch application -i 9192183 -o database:https://use1-prd-seq-hub-appdata.s3.amazonaws.com/16S_Metagenomics_v1.1/RefSeq-RDP16S_v3_May2018_DADA2_32bp.dat  -o project-id:143655512 -o sample-id:270672402

Currently I am trying with the following:

configJson = {
  "Name": "16S Metagenomics - %s" % self.sample.Id,
  "AutoStart": True,
  "Properties":
  [
    {
      "name": "Input.project-id",
      "Type": "project",
      "Content": "v1pre3/projects/%s" % self.bsapi.projectId
    },
    {
      "name": "Input.sample-id",
      "Type": "sample[]",
      "items": ["v1pre3/samples/%s" % self.sample.Id]
    },
    {
      "name": "Input.database",
      "Type": "database",
      "Content": "https://use1-prd-seq-hub-appdata.s3.amazonaws.com/16S_Metagenomics_v1.1/RefSeq-RDP16S_v3_May2018_DADA2_32bp.dat"
    }
  ]
}

But I am having difficult passing in the database value.

I get this error message:

'ErrorCode': 'BASESPACE.PROPERTIES.TYPE_UNSUPPORTED', 'Message': "The given type 'database' is not currently supported by properties."}

many thanks!

On Saturday, 12 December 2020 19:17:07 UTC, Nick Vinckier wrote:

Hi Ross,

From the look of that URL this might be a Classic Sample ID (from an older version of the BaseSpace API), whereas the app may be expecting it's BioSample ID (which is different and part of the New BaseSpace API). You can either switch your BaseSpace Application version (in Settings) to New and get the BioSample ID from the URL when on the BioSample page for BS1-FUR86. Or, and perhaps more helpful, you can list your biosamples and either grep for that BioSample, or use the BaseSpace CLI --filter-term and --filter-field. Or, you can narrow the list of BioSamples returned by limiting to a specific project ID with the --project-id.

Hopefully that helps, if you're still hitting issues, I might suggest emailing techs...@illumina.com if you've not already done so.

Cheers,

Nick

On Fri, Dec 11, 2020 at 10:02 AM Ross via basespace-developers <basespace-developers+APn2wQd4sdeDznjETe3UMAQl3ZGxyQYwYaUO...@googlegroups.com> wrote:

Hello,

"Failed getting biosample with ID 311754778: BASESPACE.COMMON.NOT_FOUND: Resource not found at the given path"

I get the above error when I try to launch a basespace app as follows:

bs launch application -i 9192183 -o database:https://use1-prd-seq-hub-appdata.s3.amazonaws.com/16S_Metagenomics_v1.1/RefSeq-RDP16S_v3_May2018_DADA2_32bp.dat  -o project-id:143655512 -o sample-id:311754778

I have obtained the sample-id from the URL in basespace:

https://basespace.illumina.com/sample/311754778/BS1-FUR86

Using the same CLI settings, I have managed to download the sample using it's name BS1-FUR86 but not using it's ID. Am I not using the correct ID? The app I'm calling doesn't take name so I can't use that.

Any ideas why it's not finding the sample using it's ID as per the URL?

thank you

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[Nick Vinckier]

Hi Ross,

I'm not sure if it will help/work, but if you run that CLI command and add -vvvvv you will get a very verbose output, within which will be the curl command used to got the API along with the form data in JSON format. It's a single line JSON, but you should be able to get the key/value pairs you need.

It could be app specific what you get back, so hopefully that will work for you.

Cheers,

Nick

On Fri, Dec 11, 2020 at 10:02 AM Ross via basespace-developers <basespace-developers+APn2wQd4sde...@googlegroups.com> wrote:

Hello,

"Failed getting biosample with ID 311754778: BASESPACE.COMMON.NOT_FOUND: Resource not found at the given path"

I get the above error when I try to launch a basespace app as follows:

bs launch application -i 9192183 -o database:https://use1-prd-seq-hub-appdata.s3.amazonaws.com/16S_Metagenomics_v1.1/RefSeq-RDP16S_v3_May2018_DADA2_32bp.dat  -o project-id:143655512 -o sample-id:311754778

I have obtained the sample-id from the URL in basespace:

https://basespace.illumina.com/sample/311754778/BS1-FUR86

Using the same CLI settings, I have managed to download the sample using it's name BS1-FUR86 but not using it's ID. Am I not using the correct ID? The app I'm calling doesn't take name so I can't use that.

Any ideas why it's not finding the sample using it's ID as per the URL?

thank you

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[Ross]

Hi Nick,

thanks so much. I managed to get it working. here's the solution in case anyone else needs this. So the database parameter is correct but no type is needed, so just like this works:

configJson = {
"Name": "16S Metagenomics - %s" % self.sample.Id,
"AutoStart": True,
"Properties":
[
{
"name": "Input.project-id",
"Type": "project",
"Content": "v1pre3/projects/%s" % self.bsapi.projectId
},
{
"name": "Input.sample-id",
"Type": "sample[]",
"items": ["v1pre3/samples/%s" % self.sample.Id],

},
{
"name": "Input.database",
"Content": "https://use1-prd-seq-hub-appdata.s3.amazonaws.com/16S_Metagenomics_v1.1/RefSeq-RDP16S_v3_May2018_DADA2_32bp.dat"
}
]
}

[Nick Vinckier]

Hi Ross,

That's great to know, thanks for posting for the community. Did using the verbose option with the CLI help with that, or did you just give it a shot without the type key?

Cheers,

Nick

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