sequence_stores

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

Overview

Name	sequence_stores
Type	Resource
Id	aws.omics.sequence_stores

Fields

The following fields are returned by SELECT queries:

get_sequence_store

Name	Datatype	Description
id	string	The store's ID. (pattern: <code>[0-9]+</code>)
name	string	The store's name. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
arn	string	The store's ARN. (pattern: <code>arn:.+</code>)
creation_time	string (date-time)	When the store was created.
description	string	The store's description. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
e_tag_algorithm_family	string	The algorithm family of the ETag. (MD5up, SHA256up, SHA512up)
fallback_location	string	An S3 location that is used to store files that have failed a direct upload. (pattern: <code>$|^s3:​//([a-z0-9][a-z0-9-.]{1,61}[a-z0-9])/?((.{1,1024})/)?</code>)
propagated_set_level_tags	array	The tags keys to propagate to the S3 objects associated with read sets in the sequence store.
s_3_access	object	The S3 access metadata of the sequence store.
sse_config	object	Server-side encryption (SSE) settings for a store.
status	string	The status of the sequence store. (CREATING, ACTIVE, UPDATING, DELETING, FAILED)
status_message	string	The status message of the sequence store. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
update_time	string (date-time)	The last-updated time of the sequence store.

list_sequence_stores

Name	Datatype	Description
id	string	The store's ID. (pattern: <code>[0-9]+</code>)
name	string	The store's name. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
arn	string	The store's ARN. (pattern: <code>arn:.+</code>)
creation_time	string (date-time)	When the store was created.
description	string	The store's description. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
e_tag_algorithm_family	string	The algorithm family of the ETag. (MD5up, SHA256up, SHA512up)
fallback_location	string	An S3 location that is used to store files that have failed a direct upload. (pattern: <code>$|^s3:​//([a-z0-9][a-z0-9-.]{1,61}[a-z0-9])/?((.{1,1024})/)?</code>)
sse_config	object	Server-side encryption (SSE) settings for a store.
status	string	Status of the sequence store. (CREATING, ACTIVE, UPDATING, DELETING, FAILED)
status_message	string	The status message of the sequence store. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
update_time	string (date-time)	The last-updated time of the Sequence Store.

Methods

The following methods are available for this resource:

Name	Accessible by	Required Params	Optional Params	Description
get_sequence_store	select	id, region		Retrieves metadata for a sequence store using its ID and returns it in JSON format.
list_sequence_stores	select	region	maxResults, nextToken	Retrieves a list of sequence stores and returns each sequence store's metadata. For more information, see Creating a HealthOmics sequence store in the Amazon Web Services HealthOmics User Guide.
create_sequence_store	insert	region, name		Creates a sequence store and returns its metadata. Sequence stores are used to store sequence data files called read sets that are saved in FASTQ, BAM, uBAM, or CRAM formats. For aligned formats (BAM and CRAM), a sequence store can only use one reference genome. For unaligned formats (FASTQ and uBAM), a reference genome is not required. You can create multiple sequence stores per region per account. The following are optional parameters you can specify for your sequence store: Use s3AccessConfig to configure your sequence store with S3 access logs (recommended). Use sseConfig to define your own KMS key for encryption. Use eTagAlgorithmFamily to define which algorithm to use for the HealthOmics eTag on objects. Use fallbackLocation to define a backup location for storing files that have failed a direct upload. Use propagatedSetLevelTags to configure tags that propagate to all objects in your store. For more information, see Creating a HealthOmics sequence store in the Amazon Web Services HealthOmics User Guide.
update_sequence_store	update	id, region		Update one or more parameters for the sequence store.
delete_sequence_store	delete	id, region		Deletes a sequence store and returns a response with no body if the operation is successful. You can only delete a sequence store when it does not contain any read sets. Use the BatchDeleteReadSet API operation to ensure that all read sets in the sequence store are deleted. When a sequence store is deleted, all tags associated with the store are also deleted. For more information, see Deleting HealthOmics reference and sequence stores in the Amazon Web Services HealthOmics User Guide.
abort_multipart_read_set_upload	exec	sequence_store_id, upload_id, region		Stops a multipart read set upload into a sequence store and returns a response with no body if the operation is successful. To confirm that a multipart read set upload has been stopped, use the ListMultipartReadSetUploads API operation to view all active multipart read set uploads.
complete_multipart_read_set_upload	exec	sequence_store_id, upload_id, region, parts		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.
upload_read_set_part	exec	sequence_store_id, upload_id, partSource, partNumber, region, payload		Uploads a specific part of a read set into a sequence store. When you a upload a read set part with a part number that already exists, the new part replaces the existing one. This operation returns a JSON formatted response containing a string identifier that is used to confirm that parts are being added to the intended upload. For more information, see Direct upload to a sequence store in the Amazon Web Services HealthOmics User Guide.

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 sequence store's ID.
partNumber	integer	The number of the part being uploaded.
partSource	string	The source file for an upload part.
region	string	AWS region (default: us-east-1)
sequence_store_id	string	The Sequence Store ID used for the multipart upload.
upload_id	string	The ID for the initiated multipart upload.
maxResults	integer	The maximum number of stores 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_sequence_store

Retrieves metadata for a sequence store using its ID and returns it in JSON format.

SELECT
id,
name,
arn,
creation_time,
description,
e_tag_algorithm_family,
fallback_location,
propagated_set_level_tags,
s_3_access,
sse_config,
status,
status_message,
update_time
FROM aws.omics.sequence_stores
WHERE id = '{{ id }}' -- required
AND region = '{{ region }}' -- required
;

list_sequence_stores

Retrieves a list of sequence stores and returns each sequence store's metadata. For more information, see Creating a HealthOmics sequence store in the Amazon Web Services HealthOmics User Guide.

SELECT
id,
name,
arn,
creation_time,
description,
e_tag_algorithm_family,
fallback_location,
sse_config,
status,
status_message,
update_time
FROM aws.omics.sequence_stores
WHERE region = '{{ region }}' -- required
AND maxResults = '{{ maxResults }}'
AND nextToken = '{{ nextToken }}'
;

INSERT examples

create_sequence_store

Creates a sequence store and returns its metadata. Sequence stores are used to store sequence data files called read sets that are saved in FASTQ, BAM, uBAM, or CRAM formats. For aligned formats (BAM and CRAM), a sequence store can only use one reference genome. For unaligned formats (FASTQ and uBAM), a reference genome is not required. You can create multiple sequence stores per region per account. The following are optional parameters you can specify for your sequence store: Use s3AccessConfig to configure your sequence store with S3 access logs (recommended). Use sseConfig to define your own KMS key for encryption. Use eTagAlgorithmFamily to define which algorithm to use for the HealthOmics eTag on objects. Use fallbackLocation to define a backup location for storing files that have failed a direct upload. Use propagatedSetLevelTags to configure tags that propagate to all objects in your store. For more information, see Creating a HealthOmics sequence store in the Amazon Web Services HealthOmics User Guide.

INSERT INTO aws.omics.sequence_stores (
name,
description,
sseConfig,
tags,
clientToken,
fallbackLocation,
eTagAlgorithmFamily,
propagatedSetLevelTags,
s3AccessConfig,
region
)
SELECT 
'{{ name }}' /* required */,
'{{ description }}',
'{{ sseConfig }}',
'{{ tags }}',
'{{ clientToken }}',
'{{ fallbackLocation }}',
'{{ eTagAlgorithmFamily }}',
'{{ propagatedSetLevelTags }}',
'{{ s3AccessConfig }}',
'{{ region }}'
RETURNING
id,
name,
arn,
creation_time,
description,
e_tag_algorithm_family,
fallback_location,
propagated_set_level_tags,
s_3_access,
sse_config,
status,
status_message
;

Manifest

# Description fields are for documentation purposes
- name: sequence_stores
props:
  - name: region
    value: "{{ region }}"
    description: Required parameter for the sequence_stores resource.
  - name: name
    value: "{{ name }}"
  - name: description
    value: "{{ description }}"
  - name: sseConfig
    description: |
      Server-side encryption (SSE) settings for a store.
    value:
      type_: "{{ type_ }}"
      keyArn: "{{ keyArn }}"
  - name: tags
    value: "{{ tags }}"
  - name: clientToken
    value: "{{ clientToken }}"
  - name: fallbackLocation
    value: "{{ fallbackLocation }}"
  - name: eTagAlgorithmFamily
    value: "{{ eTagAlgorithmFamily }}"
    valid_values: ['MD5up', 'SHA256up', 'SHA512up']
  - name: propagatedSetLevelTags
    value:
      - "{{ propagatedSetLevelTags }}"
  - name: s3AccessConfig
    description: |
      S3 access configuration parameters.
    value:
      accessLogLocation: "{{ accessLogLocation }}"

UPDATE examples

update_sequence_store

Update one or more parameters for the sequence store.

UPDATE aws.omics.sequence_stores
SET 
name = '{{ name }}',
description = '{{ description }}',
clientToken = '{{ clientToken }}',
fallbackLocation = '{{ fallbackLocation }}',
propagatedSetLevelTags = '{{ propagatedSetLevelTags }}',
s3AccessConfig = '{{ s3AccessConfig }}'
WHERE 
id = '{{ id }}' --required
AND region = '{{ region }}' --required
RETURNING
id,
name,
arn,
creation_time,
description,
e_tag_algorithm_family,
fallback_location,
propagated_set_level_tags,
s_3_access,
sse_config,
status,
status_message,
update_time;

DELETE examples

delete_sequence_store

Deletes a sequence store and returns a response with no body if the operation is successful. You can only delete a sequence store when it does not contain any read sets. Use the BatchDeleteReadSet API operation to ensure that all read sets in the sequence store are deleted. When a sequence store is deleted, all tags associated with the store are also deleted. For more information, see Deleting HealthOmics reference and sequence stores in the Amazon Web Services HealthOmics User Guide.

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

Lifecycle Methods

abort_multipart_read_set_upload

Stops a multipart read set upload into a sequence store and returns a response with no body if the operation is successful. To confirm that a multipart read set upload has been stopped, use the ListMultipartReadSetUploads API operation to view all active multipart read set uploads.

EXEC aws.omics.sequence_stores.abort_multipart_read_set_upload 
@sequence_store_id='{{ sequence_store_id }}' --required, 
@upload_id='{{ upload_id }}' --required, 
@region='{{ region }}' --required
;

complete_multipart_read_set_upload

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.

EXEC aws.omics.sequence_stores.complete_multipart_read_set_upload 
@sequence_store_id='{{ sequence_store_id }}' --required, 
@upload_id='{{ upload_id }}' --required, 
@region='{{ region }}' --required 
@@json=
'{
"parts": "{{ parts }}"
}'
;

upload_read_set_part

Uploads a specific part of a read set into a sequence store. When you a upload a read set part with a part number that already exists, the new part replaces the existing one. This operation returns a JSON formatted response containing a string identifier that is used to confirm that parts are being added to the intended upload. For more information, see Direct upload to a sequence store in the Amazon Web Services HealthOmics User Guide.

EXEC aws.omics.sequence_stores.upload_read_set_part 
@sequence_store_id='{{ sequence_store_id }}' --required, 
@upload_id='{{ upload_id }}' --required, 
@partSource='{{ partSource }}' --required, 
@partNumber='{{ partNumber }}' --required, 
@region='{{ region }}' --required 
@@json=
'{
"payload": "{{ payload }}"
}'
;