references

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

Overview

Name	references
Type	Resource
Id	aws.omics.references

Fields

The following fields are returned by SELECT queries:

get_reference

Name	Datatype	Description
payload	string (byte)	The reference file payload.

list_references

Name	Datatype	Description
id	string	The reference's ID. (pattern: <code>[0-9]+</code>)
name	string	The reference's name. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
arn	string	The reference's ARN. (pattern: <code>arn:.+</code>)
creation_time	string (date-time)	When the reference was created.
description	string	The reference's description. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
md_5	string	The reference's MD5 checksum. (pattern: <code>[\p{L}||\p{N}]+</code>)
reference_store_id	string	The reference's store ID. (pattern: <code>[0-9]+</code>)
status	string	The reference's status. (ACTIVE, DELETING, DELETED)
update_time	string (date-time)	When the reference was updated.

Methods

The following methods are available for this resource:

Name	Accessible by	Required Params	Optional Params	Description
get_reference	select	id, reference_store_id, partNumber, region	Range, file	Downloads parts of data from a reference genome and returns the reference file in the same format that it was uploaded. For more information, see Creating a HealthOmics reference store in the Amazon Web Services HealthOmics User Guide.
list_references	select	reference_store_id, region	maxResults, nextToken	Retrieves the metadata of one or more reference genomes in a reference store. For more information, see Creating a reference store in the Amazon Web Services HealthOmics User Guide.
delete_reference	delete	id, reference_store_id, region		Deletes a reference genome and returns a response with no body if the operation is successful. The read set associated with the reference genome must first be deleted before deleting the reference genome. After the reference genome is deleted, you can delete the reference store using the DeleteReferenceStore API operation. For more information, see Deleting HealthOmics reference and sequence stores in the Amazon Web Services HealthOmics User Guide.
start_reference_import_job	exec	reference_store_id, region, roleArn, sources		Imports a reference genome from Amazon S3 into a specified reference store. You can have multiple reference genomes in a reference store. You can only import reference genomes one at a time into each reference store. Monitor the status of your reference import job by using the GetReferenceImportJob 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 reference's ID.
partNumber	integer	The part number to retrieve.
reference_store_id	string	The job's reference store ID.
region	string	AWS region (default: us-east-1)
Range	string	The range to retrieve.
file	string	The file to retrieve.
maxResults	integer	The maximum number of references 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_reference

Downloads parts of data from a reference genome and returns the reference file in the same format that it was uploaded. For more information, see Creating a HealthOmics reference store in the Amazon Web Services HealthOmics User Guide.

SELECT
payload
FROM aws.omics.references
WHERE id = '{{ id }}' -- required
AND reference_store_id = '{{ reference_store_id }}' -- required
AND partNumber = '{{ partNumber }}' -- required
AND region = '{{ region }}' -- required
AND Range = '{{ Range }}'
AND file = '{{ file }}'
;

list_references

Retrieves the metadata of one or more reference genomes in a reference store. For more information, see Creating a reference store in the Amazon Web Services HealthOmics User Guide.

SELECT
id,
name,
arn,
creation_time,
description,
md_5,
reference_store_id,
status,
update_time
FROM aws.omics.references
WHERE reference_store_id = '{{ reference_store_id }}' -- required
AND region = '{{ region }}' -- required
AND maxResults = '{{ maxResults }}'
AND nextToken = '{{ nextToken }}'
;

DELETE examples

delete_reference

Deletes a reference genome and returns a response with no body if the operation is successful. The read set associated with the reference genome must first be deleted before deleting the reference genome. After the reference genome is deleted, you can delete the reference store using the DeleteReferenceStore API operation. For more information, see Deleting HealthOmics reference and sequence stores in the Amazon Web Services HealthOmics User Guide.

DELETE FROM aws.omics.references
WHERE id = '{{ id }}' --required
AND reference_store_id = '{{ reference_store_id }}' --required
AND region = '{{ region }}' --required
;

Lifecycle Methods

start_reference_import_job

Imports a reference genome from Amazon S3 into a specified reference store. You can have multiple reference genomes in a reference store. You can only import reference genomes one at a time into each reference store. Monitor the status of your reference import job by using the GetReferenceImportJob API operation.

EXEC aws.omics.references.start_reference_import_job 
@reference_store_id='{{ reference_store_id }}' --required, 
@region='{{ region }}' --required 
@@json=
'{
"roleArn": "{{ roleArn }}", 
"clientToken": "{{ clientToken }}", 
"sources": "{{ sources }}"
}'
;