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[ aws . omics ]

list-multipart-read-set-uploads¶

Description¶

Lists multipart read set uploads and for in progress uploads. Once the upload is completed, a read set is created and the upload will no longer be returned in the response.

Synopsis¶

  list-multipart-read-set-uploads
--sequence-store-id <value>
[--cli-input-json <value>]
[--starting-token <value>]
[--page-size <value>]
[--max-items <value>]
[--generate-cli-skeleton <value>]
[--debug]
[--endpoint-url <value>]
[--no-verify-ssl]
[--no-paginate]
[--output <value>]
[--query <value>]
[--profile <value>]
[--region <value>]
[--version <value>]
[--color <value>]
[--no-sign-request]
[--ca-bundle <value>]
[--cli-read-timeout <value>]
[--cli-connect-timeout <value>]

Options¶

--sequence-store-id (string)

The Sequence Store ID used for the multipart uploads.

--cli-input-json (string) Performs service operation based on the JSON string provided. The JSON string follows the format provided by --generate-cli-skeleton. If other arguments are provided on the command line, the CLI values will override the JSON-provided values. It is not possible to pass arbitrary binary values using a JSON-provided value as the string will be taken literally.

--starting-token (string)

A token to specify where to start paginating. This is the NextToken from a previously truncated response.

For usage examples, see Pagination in the AWS Command Line Interface User Guide .

--page-size (integer)

The size of each page to get in the AWS service call. This does not affect the number of items returned in the command's output. Setting a smaller page size results in more calls to the AWS service, retrieving fewer items in each call. This can help prevent the AWS service calls from timing out.

For usage examples, see Pagination in the AWS Command Line Interface User Guide .

--max-items (integer)

The total number of items to return in the command's output. If the total number of items available is more than the value specified, a NextToken is provided in the command's output. To resume pagination, provide the NextToken value in the starting-token argument of a subsequent command. Do not use the NextToken response element directly outside of the AWS CLI.

For usage examples, see Pagination in the AWS Command Line Interface User Guide .

--generate-cli-skeleton (string) Prints a JSON skeleton to standard output without sending an API request. If provided with no value or the value input, prints a sample input JSON that can be used as an argument for --cli-input-json. If provided with the value output, it validates the command inputs and returns a sample output JSON for that command.

Global Options¶

--debug (boolean)

Turn on debug logging.

--endpoint-url (string)

Override command's default URL with the given URL.

--no-verify-ssl (boolean)

By default, the AWS CLI uses SSL when communicating with AWS services. For each SSL connection, the AWS CLI will verify SSL certificates. This option overrides the default behavior of verifying SSL certificates.

--no-paginate (boolean)

Disable automatic pagination. If automatic pagination is disabled, the AWS CLI will only make one call, for the first page of results.

--output (string)

The formatting style for command output.

json
text
table

--query (string)

A JMESPath query to use in filtering the response data.

--profile (string)

Use a specific profile from your credential file.

--region (string)

The region to use. Overrides config/env settings.

--version (string)

Display the version of this tool.

--color (string)

Turn on/off color output.

on
off
auto

--no-sign-request (boolean)

Do not sign requests. Credentials will not be loaded if this argument is provided.

--ca-bundle (string)

The CA certificate bundle to use when verifying SSL certificates. Overrides config/env settings.

--cli-read-timeout (int)

The maximum socket read time in seconds. If the value is set to 0, the socket read will be blocking and not timeout. The default value is 60 seconds.

--cli-connect-timeout (int)

The maximum socket connect time in seconds. If the value is set to 0, the socket connect will be blocking and not timeout. The default value is 60 seconds.

Examples¶

Note

To use the following examples, you must have the AWS CLI installed and configured. See the Getting started guide in the AWS CLI User Guide for more information.

Unless otherwise stated, all examples have unix-like quotation rules. These examples will need to be adapted to your terminal's quoting rules. See Using quotation marks with strings in the AWS CLI User Guide .

To list all multipart read set uploads and their statuses.

The following list-multipart-read-set-uploads example lists all multipart read set uploads and their statuses.

aws omics list-multipart-read-set-uploads \
    --sequence-store-id 0123456789

Output:

{
"uploads":
    [
        {
           "sequenceStoreId": "0123456789",
           "uploadId": "8749584421",
           "sourceFileType": "FASTQ",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "name": "HG00146",
            "description": "FASTQ for HG00146",
            "creationTime": "2023-11-29T19:22:51.349298+00:00"
        },
        {
            "sequenceStoreId": "0123456789",
            "uploadId": "5290538638",
            "sourceFileType": "BAM",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "referenceArn": "arn:aws:omics:us-west-2:845448930428:referenceStore/8168613728/reference/2190697383",
            "name": "HG00146",
            "description": "BAM for HG00146",
            "creationTime": "2023-11-29T19:23:33.116516+00:00"
        },
        {
            "sequenceStoreId": "0123456789",
            "uploadId": "4174220862",
            "sourceFileType": "BAM",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "referenceArn": "arn:aws:omics:us-west-2:845448930428:referenceStore/8168613728/reference/2190697383",
            "name": "HG00147",
            "description": "BAM for HG00147",
            "creationTime": "2023-11-29T19:23:47.007866+00:00"
        }
    ]
}

For more information, see Direct upload to a sequence store in the AWS HealthOmics User Guide.

Output¶

nextToken -> (string)

Next token returned in the response of a previous ListMultipartReadSetUploads call. Used to get the next page of results.

uploads -> (list)

An array of multipart uploads.

(structure)

Part of the response to ListMultipartReadSetUploads, excluding completed and aborted multipart uploads.

sequenceStoreId -> (string)

The sequence store ID used for the multipart upload.

uploadId -> (string)

The ID for the initiated multipart upload.

sourceFileType -> (string)

The type of file the read set originated from.

subjectId -> (string)

The read set source's subject ID.

sampleId -> (string)

The read set source's sample ID.

generatedFrom -> (string)

The source of an uploaded part.

referenceArn -> (string)

The source's reference ARN.

name -> (string)

The name of a read set.

description -> (string)

The description of a read set.

tags -> (map)

Any tags you wish to add to a read set.

key -> (string)

value -> (string)

creationTime -> (timestamp)

The time stamp for when a direct upload was created.

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