AWS API Changes

2024/04/11 - Amazon Omics - 6 updated api methods

Changes This release adds support for retrieval of S3 direct access metadata on sequence stores and read sets, and adds support for SHA256up and SHA512up HealthOmics ETags.

CreateSequenceStore (updated)

Link ¶
Changes (both)

{'eTagAlgorithmFamily': 'MD5up | SHA256up | SHA512up'}

Creates a sequence store.

See also: AWS API Documentation

Request Syntax

client.create_sequence_store(
    name='string',
    description='string',
    sseConfig={
        'type': 'KMS',
        'keyArn': 'string'
    },
    tags={
        'string': 'string'
    },
    clientToken='string',
    fallbackLocation='string',
    eTagAlgorithmFamily='MD5up'|'SHA256up'|'SHA512up'
)

type name:

string

param name:

[REQUIRED]

A name for the store.

type description:

string

param description:

A description for the store.

type sseConfig:

dict

param sseConfig:

Server-side encryption (SSE) settings for the store.

type (string) -- [REQUIRED]

The encryption type.
keyArn (string) --

An encryption key ARN.

type tags:

dict

param tags:

Tags for the store.

(string) --
- (string) --

type clientToken:

string

param clientToken:

To ensure that requests don't run multiple times, specify a unique token for each request.

type fallbackLocation:

string

param fallbackLocation:

An S3 location that is used to store files that have failed a direct upload.

type eTagAlgorithmFamily:

string

param eTagAlgorithmFamily:

The ETag algorithm family to use for ingested read sets.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'arn': 'string',
    'name': 'string',
    'description': 'string',
    'sseConfig': {
        'type': 'KMS',
        'keyArn': 'string'
    },
    'creationTime': datetime(2015, 1, 1),
    'fallbackLocation': 'string',
    'eTagAlgorithmFamily': 'MD5up'|'SHA256up'|'SHA512up'
}

Response Structure

(dict) --
- id (string) --
  
  The store's ID.
- arn (string) --
  
  The store's ARN.
- name (string) --
  
  The store's name.
- description (string) --
  
  The store's description.
- sseConfig (dict) --
  
  The store's SSE settings.
  - type (string) --
    
    The encryption type.
  - keyArn (string) --
    
    An encryption key ARN.
- creationTime (datetime) --
  
  When the store was created.
- fallbackLocation (string) --
  
  An S3 location that is used to store files that have failed a direct upload.
- eTagAlgorithmFamily (string) --
  
  The algorithm family of the ETag.

GetReadSetMetadata (updated)

Link ¶
Changes (response)

{'etag': {'algorithm': {'BAM_SHA256up',
                        'BAM_SHA512up',
                        'CRAM_SHA256up',
                        'CRAM_SHA512up',
                        'FASTQ_SHA256up',
                        'FASTQ_SHA512up'}},
 'files': {'index': {'s3Access': {'s3Uri': 'string'}},
           'source1': {'s3Access': {'s3Uri': 'string'}},
           'source2': {'s3Access': {'s3Uri': 'string'}}}}

Gets details about a read set.

See also: AWS API Documentation

Request Syntax

client.get_read_set_metadata(
    id='string',
    sequenceStoreId='string'
)

type id:

string

param id:

[REQUIRED]

The read set's ID.

type sequenceStoreId:

string

param sequenceStoreId:

[REQUIRED]

The read set's sequence store ID.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'arn': 'string',
    'sequenceStoreId': 'string',
    'subjectId': 'string',
    'sampleId': 'string',
    'status': 'ARCHIVED'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'PROCESSING_UPLOAD'|'UPLOAD_FAILED',
    'name': 'string',
    'description': 'string',
    'fileType': 'FASTQ'|'BAM'|'CRAM'|'UBAM',
    'creationTime': datetime(2015, 1, 1),
    'sequenceInformation': {
        'totalReadCount': 123,
        'totalBaseCount': 123,
        'generatedFrom': 'string',
        'alignment': 'string'
    },
    'referenceArn': 'string',
    'files': {
        'source1': {
            'totalParts': 123,
            'partSize': 123,
            'contentLength': 123,
            's3Access': {
                's3Uri': 'string'
            }
        },
        'source2': {
            'totalParts': 123,
            'partSize': 123,
            'contentLength': 123,
            's3Access': {
                's3Uri': 'string'
            }
        },
        'index': {
            'totalParts': 123,
            'partSize': 123,
            'contentLength': 123,
            's3Access': {
                's3Uri': 'string'
            }
        }
    },
    'statusMessage': 'string',
    'creationType': 'IMPORT'|'UPLOAD',
    'etag': {
        'algorithm': 'FASTQ_MD5up'|'BAM_MD5up'|'CRAM_MD5up'|'FASTQ_SHA256up'|'BAM_SHA256up'|'CRAM_SHA256up'|'FASTQ_SHA512up'|'BAM_SHA512up'|'CRAM_SHA512up',
        'source1': 'string',
        'source2': 'string'
    }
}

Response Structure

(dict) --
- id (string) --
  
  The read set's ID.
- arn (string) --
  
  The read set's ARN.
- sequenceStoreId (string) --
  
  The read set's sequence store ID.
- subjectId (string) --
  
  The read set's subject ID.
- sampleId (string) --
  
  The read set's sample ID.
- status (string) --
  
  The read set's status.
- name (string) --
  
  The read set's name.
- description (string) --
  
  The read set's description.
- fileType (string) --
  
  The read set's file type.
- creationTime (datetime) --
  
  When the read set was created.
- sequenceInformation (dict) --
  
  The read set's sequence information.
  - totalReadCount (integer) --
    
    The sequence's total read count.
  - totalBaseCount (integer) --
    
    The sequence's total base count.
  - generatedFrom (string) --
    
    Where the sequence originated.
  - alignment (string) --
    
    The sequence's alignment setting.
- referenceArn (string) --
  
  The read set's genome reference ARN.
- files (dict) --
  
  The read set's files.
  - source1 (dict) --
    
    The location of the first file in Amazon S3.
    - totalParts (integer) --
      
      The file's total parts.
    - partSize (integer) --
      
      The file's part size.
    - contentLength (integer) --
      
      The file's content length.
    - s3Access (dict) --
      
      The S3 URI metadata of a sequence store.
      - s3Uri (string) --
        
        The S3 URI for each read set file.
  - source2 (dict) --
    
    The location of the second file in Amazon S3.
    - totalParts (integer) --
      
      The file's total parts.
    - partSize (integer) --
      
      The file's part size.
    - contentLength (integer) --
      
      The file's content length.
    - s3Access (dict) --
      
      The S3 URI metadata of a sequence store.
      - s3Uri (string) --
        
        The S3 URI for each read set file.
  - index (dict) --
    
    The files' index.
    - totalParts (integer) --
      
      The file's total parts.
    - partSize (integer) --
      
      The file's part size.
    - contentLength (integer) --
      
      The file's content length.
    - s3Access (dict) --
      
      The S3 URI metadata of a sequence store.
      - s3Uri (string) --
        
        The S3 URI for each read set file.
- statusMessage (string) --
  
  The status message for a read set. It provides more detail as to why the read set has a status.
- creationType (string) --
  
  The creation type of the read set.
- etag (dict) --
  
  The entity tag (ETag) is a hash of the object meant to represent its semantic content.
  - algorithm (string) --
    
    The algorithm used to calculate the read set’s ETag(s).
  - source1 (string) --
    
    The ETag hash calculated on Source1 of the read set.
  - source2 (string) --
    
    The ETag hash calculated on Source2 of the read set.

GetReferenceMetadata (updated)

Link ¶
Changes (response)

{'files': {'index': {'s3Access': {'s3Uri': 'string'}},
           'source': {'s3Access': {'s3Uri': 'string'}}}}

Gets information about a genome reference's metadata.

See also: AWS API Documentation

Request Syntax

client.get_reference_metadata(
    id='string',
    referenceStoreId='string'
)

type id:

string

param id:

[REQUIRED]

The reference's ID.

type referenceStoreId:

string

param referenceStoreId:

[REQUIRED]

The reference's reference store ID.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'arn': 'string',
    'referenceStoreId': 'string',
    'md5': 'string',
    'status': 'ACTIVE'|'DELETING'|'DELETED',
    'name': 'string',
    'description': 'string',
    'creationTime': datetime(2015, 1, 1),
    'updateTime': datetime(2015, 1, 1),
    'files': {
        'source': {
            'totalParts': 123,
            'partSize': 123,
            'contentLength': 123,
            's3Access': {
                's3Uri': 'string'
            }
        },
        'index': {
            'totalParts': 123,
            'partSize': 123,
            'contentLength': 123,
            's3Access': {
                's3Uri': 'string'
            }
        }
    }
}

Response Structure

(dict) --
- id (string) --
  
  The reference's ID.
- arn (string) --
  
  The reference's ARN.
- referenceStoreId (string) --
  
  The reference's reference store ID.
- md5 (string) --
  
  The reference's MD5 checksum.
- status (string) --
  
  The reference's status.
- name (string) --
  
  The reference's name.
- description (string) --
  
  The reference's description.
- creationTime (datetime) --
  
  When the reference was created.
- updateTime (datetime) --
  
  When the reference was updated.
- files (dict) --
  
  The reference's files.
  - source (dict) --
    
    The source file's location in Amazon S3.
    - totalParts (integer) --
      
      The file's total parts.
    - partSize (integer) --
      
      The file's part size.
    - contentLength (integer) --
      
      The file's content length.
    - s3Access (dict) --
      
      The S3 URI metadata of a sequence store.
      - s3Uri (string) --
        
        The S3 URI for each read set file.
  - index (dict) --
    
    The files' index.
    - totalParts (integer) --
      
      The file's total parts.
    - partSize (integer) --
      
      The file's part size.
    - contentLength (integer) --
      
      The file's content length.
    - s3Access (dict) --
      
      The S3 URI metadata of a sequence store.
      - s3Uri (string) --
        
        The S3 URI for each read set file.

GetSequenceStore (updated)

Link ¶
Changes (response)

{'eTagAlgorithmFamily': 'MD5up | SHA256up | SHA512up',
 's3Access': {'s3AccessPointArn': 'string', 's3Uri': 'string'}}

Gets information about a sequence store.

See also: AWS API Documentation

Request Syntax

client.get_sequence_store(
    id='string'
)

type id:

string

param id:

[REQUIRED]

The store's ID.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'arn': 'string',
    'name': 'string',
    'description': 'string',
    'sseConfig': {
        'type': 'KMS',
        'keyArn': 'string'
    },
    'creationTime': datetime(2015, 1, 1),
    'fallbackLocation': 'string',
    's3Access': {
        's3Uri': 'string',
        's3AccessPointArn': 'string'
    },
    'eTagAlgorithmFamily': 'MD5up'|'SHA256up'|'SHA512up'
}

Response Structure

(dict) --
- id (string) --
  
  The store's ID.
- arn (string) --
  
  The store's ARN.
- name (string) --
  
  The store's name.
- description (string) --
  
  The store's description.
- sseConfig (dict) --
  
  The store's server-side encryption (SSE) settings.
  - type (string) --
    
    The encryption type.
  - keyArn (string) --
    
    An encryption key ARN.
- creationTime (datetime) --
  
  When the store was created.
- fallbackLocation (string) --
  
  An S3 location that is used to store files that have failed a direct upload.
- s3Access (dict) --
  
  The S3 metadata of a sequence store, including the ARN and S3 URI of the S3 bucket.
  - s3Uri (string) --
    
    The S3 URI of the sequence store.
  - s3AccessPointArn (string) --
    
    This is ARN of the access point associated with the S3 bucket storing read sets.
- eTagAlgorithmFamily (string) --
  
  The algorithm family of the ETag.

ListReadSets (updated)

Link ¶
Changes (response)

{'readSets': {'etag': {'algorithm': {'BAM_SHA256up',
                                     'BAM_SHA512up',
                                     'CRAM_SHA256up',
                                     'CRAM_SHA512up',
                                     'FASTQ_SHA256up',
                                     'FASTQ_SHA512up'}}}}

Retrieves a list of read sets.

See also: AWS API Documentation

Request Syntax

client.list_read_sets(
    sequenceStoreId='string',
    maxResults=123,
    nextToken='string',
    filter={
        'name': 'string',
        'status': 'ARCHIVED'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'PROCESSING_UPLOAD'|'UPLOAD_FAILED',
        'referenceArn': 'string',
        'createdAfter': datetime(2015, 1, 1),
        'createdBefore': datetime(2015, 1, 1),
        'sampleId': 'string',
        'subjectId': 'string',
        'generatedFrom': 'string',
        'creationType': 'IMPORT'|'UPLOAD'
    }
)

type sequenceStoreId:

string

param sequenceStoreId:

[REQUIRED]

The jobs' sequence store ID.

type maxResults:

integer

param maxResults:

The maximum number of read sets to return in one page of results.

type nextToken:

string

param nextToken:

Specify the pagination token from a previous request to retrieve the next page of results.

type filter:

dict

param filter:

A filter to apply to the list.

name (string) --

A name to filter on.
status (string) --

A status to filter on.
referenceArn (string) --

A genome reference ARN to filter on.
createdAfter (datetime) --

The filter's start date.
createdBefore (datetime) --

The filter's end date.
sampleId (string) --

The read set source's sample ID.
subjectId (string) --

The read set source's subject ID.
generatedFrom (string) --

Where the source originated.
creationType (string) --

The creation type of the read set.

rtype:

dict

returns:

Response Syntax

{
    'nextToken': 'string',
    'readSets': [
        {
            'id': 'string',
            'arn': 'string',
            'sequenceStoreId': 'string',
            'subjectId': 'string',
            'sampleId': 'string',
            'status': 'ARCHIVED'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'PROCESSING_UPLOAD'|'UPLOAD_FAILED',
            'name': 'string',
            'description': 'string',
            'referenceArn': 'string',
            'fileType': 'FASTQ'|'BAM'|'CRAM'|'UBAM',
            'sequenceInformation': {
                'totalReadCount': 123,
                'totalBaseCount': 123,
                'generatedFrom': 'string',
                'alignment': 'string'
            },
            'creationTime': datetime(2015, 1, 1),
            'statusMessage': 'string',
            'creationType': 'IMPORT'|'UPLOAD',
            'etag': {
                'algorithm': 'FASTQ_MD5up'|'BAM_MD5up'|'CRAM_MD5up'|'FASTQ_SHA256up'|'BAM_SHA256up'|'CRAM_SHA256up'|'FASTQ_SHA512up'|'BAM_SHA512up'|'CRAM_SHA512up',
                'source1': 'string',
                'source2': 'string'
            }
        },
    ]
}

Response Structure

(dict) --
- nextToken (string) --
  
  A pagination token that's included if more results are available.
- readSets (list) --
  
  A list of read sets.
  - (dict) --
    
    A read set.
    - id (string) --
      
      The read set's ID.
    - arn (string) --
      
      The read set's ARN.
    - sequenceStoreId (string) --
      
      The read set's sequence store ID.
    - subjectId (string) --
      
      The read set's subject ID.
    - sampleId (string) --
      
      The read set's sample ID.
    - status (string) --
      
      The read set's status.
    - name (string) --
      
      The read set's name.
    - description (string) --
      
      The read set's description.
    - referenceArn (string) --
      
      The read set's genome reference ARN.
    - fileType (string) --
      
      The read set's file type.
    - sequenceInformation (dict) --
      
      Details about a sequence.
      - totalReadCount (integer) --
        
        The sequence's total read count.
      - totalBaseCount (integer) --
        
        The sequence's total base count.
      - generatedFrom (string) --
        
        Where the sequence originated.
      - alignment (string) --
        
        The sequence's alignment setting.
    - creationTime (datetime) --
      
      When the read set was created.
    - statusMessage (string) --
      
      The status for a read set. It provides more detail as to why the read set has a status.
    - creationType (string) --
      
      The creation type of the read set.
    - etag (dict) --
      
      The entity tag (ETag) is a hash of the object representing its semantic content.
      - algorithm (string) --
        
        The algorithm used to calculate the read set’s ETag(s).
      - source1 (string) --
        
        The ETag hash calculated on Source1 of the read set.
      - source2 (string) --
        
        The ETag hash calculated on Source2 of the read set.

ListSequenceStores (updated)

Link ¶
Changes (response)

{'sequenceStores': {'eTagAlgorithmFamily': 'MD5up | SHA256up | SHA512up'}}

Retrieves a list of sequence stores.

See also: AWS API Documentation

Request Syntax

client.list_sequence_stores(
    maxResults=123,
    nextToken='string',
    filter={
        'name': 'string',
        'createdAfter': datetime(2015, 1, 1),
        'createdBefore': datetime(2015, 1, 1)
    }
)

type maxResults:

integer

param maxResults:

The maximum number of stores to return in one page of results.

type nextToken:

string

param nextToken:

Specify the pagination token from a previous request to retrieve the next page of results.

type filter:

dict

param filter:

A filter to apply to the list.

name (string) --

A name to filter on.
createdAfter (datetime) --

The filter's start date.
createdBefore (datetime) --

The filter's end date.

rtype:

dict

returns:

Response Syntax

{
    'nextToken': 'string',
    'sequenceStores': [
        {
            'arn': 'string',
            'id': 'string',
            'name': 'string',
            'description': 'string',
            'sseConfig': {
                'type': 'KMS',
                'keyArn': 'string'
            },
            'creationTime': datetime(2015, 1, 1),
            'fallbackLocation': 'string',
            'eTagAlgorithmFamily': 'MD5up'|'SHA256up'|'SHA512up'
        },
    ]
}

Response Structure

(dict) --
- nextToken (string) --
  
  A pagination token that's included if more results are available.
- sequenceStores (list) --
  
  A list of sequence stores.
  - (dict) --
    
    Details about a sequence store.
    - arn (string) --
      
      The store's ARN.
    - id (string) --
      
      The store's ID.
    - name (string) --
      
      The store's name.
    - description (string) --
      
      The store's description.
    - sseConfig (dict) --
      
      The store's server-side encryption (SSE) settings.
      - type (string) --
        
        The encryption type.
      - keyArn (string) --
        
        An encryption key ARN.
    - creationTime (datetime) --
      
      When the store was created.
    - fallbackLocation (string) --
      
      An S3 location that is used to store files that have failed a direct upload.
    - eTagAlgorithmFamily (string) --
      
      The algorithm family of the ETag.