read_sets

Creates, updates, deletes, gets or lists a read_sets resource.

Overview

Name	read_sets
Type	Resource
Id	aws.omics.read_sets

Fields

The following fields are returned by SELECT queries:

get_read_set

Name	Datatype	Description
payload	string (byte)	The read set file payload.

list_read_sets

Name	Datatype	Description
id	string	The read set's ID. (pattern: <code>[0-9]+</code>)
name	string	The read set's name. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
arn	string	The read set's ARN. (pattern: <code>arn:.+</code>)
creation_time	string (date-time)	When the read set was created.
creation_type	string	The creation type of the read set. (IMPORT, UPLOAD)
description	string	The read set's description. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
etag	object	The entity tag (ETag) is a hash of the object representing its semantic content.
file_type	string	The read set's file type. (FASTQ, BAM, CRAM, UBAM)
reference_arn	string	The read set's genome reference ARN. (pattern: <code>arn:.+</code>)
sample_id	string	The read set's sample ID. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
sequence_information	object	Details about a sequence.
sequence_store_id	string	The read set's sequence store ID. (pattern: <code>[0-9]+</code>)
status	string	The read set's status. (ARCHIVED, ACTIVATING, ACTIVE, DELETING, DELETED, PROCESSING_UPLOAD, UPLOAD_FAILED)
status_message	string	The status for a read set. It provides more detail as to why the read set has a status. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
subject_id	string	The read set's subject ID. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)

Methods

The following methods are available for this resource:

Name	Accessible by	Required Params	Optional Params	Description
get_read_set	select	id, sequence_store_id, partNumber, region	file	Retrieves detailed information from parts of a read set and returns the read set in the same format that it was uploaded. You must have read sets uploaded to your sequence store in order to run this operation.
list_read_sets	select	sequence_store_id, region	maxResults, nextToken	Retrieves a list of read sets from a sequence store ID and returns the metadata in JSON format.
start_read_set_activation_job	exec	sequence_store_id, region, sources		Activates an archived read set and returns its metadata in a JSON formatted output. AWS HealthOmics automatically archives unused read sets after 30 days. To monitor the status of your read set activation job, use the GetReadSetActivationJob operation. To learn more, see Activating read sets in the Amazon Web Services HealthOmics User Guide.
start_read_set_export_job	exec	sequence_store_id, region, destination, roleArn, sources		Starts a read set export job. When the export job is finished, the read set is exported to an Amazon S3 bucket which can be retrieved using the GetReadSetExportJob API operation. To monitor the status of the export job, use the ListReadSetExportJobs API operation.
start_read_set_import_job	exec	sequence_store_id, region, roleArn, sources		Imports a read set from the sequence store. Read set import jobs support a maximum of 100 read sets of different types. Monitor the progress of your read set import job by calling the GetReadSetImportJob API operation.

Parameters

Parameters can be passed in the WHERE clause of a query. Check the Methods section to see which parameters are required or optional for each operation.

Name	Datatype	Description
id	string	The read set's ID.
partNumber	integer	The part number to retrieve.
region	string	AWS region (default: us-east-1)
sequence_store_id	string	The read set's sequence store ID.
file	string	The file to retrieve.
maxResults	integer	The maximum number of read sets to return in one page of results.
nextToken	string	Specify the pagination token from a previous request to retrieve the next page of results.

SELECT examples

get_read_set

Retrieves detailed information from parts of a read set and returns the read set in the same format that it was uploaded. You must have read sets uploaded to your sequence store in order to run this operation.

SELECT
payload
FROM aws.omics.read_sets
WHERE id = '{{ id }}' -- required
AND sequence_store_id = '{{ sequence_store_id }}' -- required
AND partNumber = '{{ partNumber }}' -- required
AND region = '{{ region }}' -- required
AND file = '{{ file }}'
;

list_read_sets

Retrieves a list of read sets from a sequence store ID and returns the metadata in JSON format.

SELECT
id,
name,
arn,
creation_time,
creation_type,
description,
etag,
file_type,
reference_arn,
sample_id,
sequence_information,
sequence_store_id,
status,
status_message,
subject_id
FROM aws.omics.read_sets
WHERE sequence_store_id = '{{ sequence_store_id }}' -- required
AND region = '{{ region }}' -- required
AND maxResults = '{{ maxResults }}'
AND nextToken = '{{ nextToken }}'
;

Lifecycle Methods

start_read_set_activation_job

Activates an archived read set and returns its metadata in a JSON formatted output. AWS HealthOmics automatically archives unused read sets after 30 days. To monitor the status of your read set activation job, use the GetReadSetActivationJob operation. To learn more, see Activating read sets in the Amazon Web Services HealthOmics User Guide.

EXEC aws.omics.read_sets.start_read_set_activation_job 
@sequence_store_id='{{ sequence_store_id }}' --required, 
@region='{{ region }}' --required 
@@json=
'{
"clientToken": "{{ clientToken }}", 
"sources": "{{ sources }}"
}'
;

start_read_set_export_job

Starts a read set export job. When the export job is finished, the read set is exported to an Amazon S3 bucket which can be retrieved using the GetReadSetExportJob API operation. To monitor the status of the export job, use the ListReadSetExportJobs API operation.

EXEC aws.omics.read_sets.start_read_set_export_job 
@sequence_store_id='{{ sequence_store_id }}' --required, 
@region='{{ region }}' --required 
@@json=
'{
"destination": "{{ destination }}", 
"roleArn": "{{ roleArn }}", 
"clientToken": "{{ clientToken }}", 
"sources": "{{ sources }}"
}'
;

start_read_set_import_job

Imports a read set from the sequence store. Read set import jobs support a maximum of 100 read sets of different types. Monitor the progress of your read set import job by calling the GetReadSetImportJob API operation.

EXEC aws.omics.read_sets.start_read_set_import_job 
@sequence_store_id='{{ sequence_store_id }}' --required, 
@region='{{ region }}' --required 
@@json=
'{
"roleArn": "{{ roleArn }}", 
"clientToken": "{{ clientToken }}", 
"sources": "{{ sources }}"
}'
;