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[ aws . omics ]

complete-multipart-read-set-upload¶

Description¶

Completes a multipart read set upload into a sequence store after you have initiated the upload process with CreateMultipartReadSetUpload and uploaded all read set parts using UploadReadSetPart . You must specify the parts you uploaded using the parts parameter. If the operation is successful, it returns the read set ID(s) of the uploaded read set(s).

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

Synopsis¶

  complete-multipart-read-set-upload
--sequence-store-id <value>
--upload-id <value>
--parts <value>
[--cli-input-json <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>]
[--v2-debug]

Options¶

--sequence-store-id (string)

The sequence store ID for the store involved in the multipart upload.

--upload-id (string)

The ID for the multipart upload.

--parts (list)

The individual uploads or parts of a multipart upload.

(structure)

Part of the response to the CompleteReadSetUpload API, including metadata.

partNumber -> (integer)

A number identifying the part in a read set upload.

partSource -> (string)

The source file of the part being uploaded.

checksum -> (string)

A unique identifier used to confirm that parts are being added to the correct upload.

Shorthand Syntax:

partNumber=integer,partSource=string,checksum=string ...

JSON Syntax:

[
  {
    "partNumber": integer,
    "partSource": "SOURCE1"|"SOURCE2",
    "checksum": "string"
  }
  ...
]

--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.

--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.

--v2-debug (boolean)

Enable AWS CLI v2 migration assistance. Prints warnings if the command would face a breaking change after swapping AWS CLI v1 for AWS CLI v2 in the current environment. Prints one warning for each breaking change detected.

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 conclude a multipart upload once you have uploaded all of the components.

The following complete-multipart-read-set-upload example concludes a multipart upload into a sequence store once all of the components have been uploaded.

aws omics complete-multipart-read-set-upload \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455 \
    --parts '[{"checksum":"gaCBQMe+rpCFZxLpoP6gydBoXaKKDA/Vobh5zBDb4W4=","partNumber":1,"partSource":"SOURCE1"}]'

Output:

{
    "readSetId": "0000000001"
    "readSetId": "0000000002"
    "readSetId": "0000000003"
}

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

Output¶

readSetId -> (string)

The read set ID created for an uploaded read set.

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