AWS API Changes

2023/10/05 - Amazon Omics - 2 updated api methods

Changes Add Etag Support for Omics Storage in ListReadSets and GetReadSetMetadata API

GetReadSetMetadata (updated)

Link ¶
Changes (response)

{'etag': {'algorithm': 'FASTQ_MD5up | BAM_MD5up | CRAM_MD5up',
          'source1': 'string',
          'source2': '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',
    'creationTime': datetime(2015, 1, 1),
    'sequenceInformation': {
        'totalReadCount': 123,
        'totalBaseCount': 123,
        'generatedFrom': 'string',
        'alignment': 'string'
    },
    'referenceArn': 'string',
    'files': {
        'source1': {
            'totalParts': 123,
            'partSize': 123,
            'contentLength': 123
        },
        'source2': {
            'totalParts': 123,
            'partSize': 123,
            'contentLength': 123
        },
        'index': {
            'totalParts': 123,
            'partSize': 123,
            'contentLength': 123
        }
    },
    'statusMessage': 'string',
    'creationType': 'IMPORT'|'UPLOAD',
    'etag': {
        'algorithm': 'FASTQ_MD5up'|'BAM_MD5up'|'CRAM_MD5up',
        '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.
  - 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.
  - 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.
- 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.

ListReadSets (updated)

Link ¶
Changes (response)

{'readSets': {'etag': {'algorithm': 'FASTQ_MD5up | BAM_MD5up | CRAM_MD5up',
                       'source1': 'string',
                       'source2': 'string'}}}

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',
            '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',
                '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.