AWS API Changes

2023/11/09 - Amazon Omics - 6 updated api methods

Changes Support UBAM filetype for Omics Storage and make referenceArn optional

CreateMultipartReadSetUpload (updated)

Link ¶
Changes (both)

{'sourceFileType': {'UBAM'}}

Begins a multipart read set upload.

See also: AWS API Documentation

Request Syntax

client.create_multipart_read_set_upload(
    sequenceStoreId='string',
    clientToken='string',
    sourceFileType='FASTQ'|'BAM'|'CRAM'|'UBAM',
    subjectId='string',
    sampleId='string',
    generatedFrom='string',
    referenceArn='string',
    name='string',
    description='string',
    tags={
        'string': 'string'
    }
)

type sequenceStoreId:

string

param sequenceStoreId:

[REQUIRED]

The sequence store ID for the store that is the destination of the multipart uploads.

type clientToken:

string

param clientToken:

An idempotency token that can be used to avoid triggering multiple multipart uploads.

type sourceFileType:

string

param sourceFileType:

[REQUIRED]

The type of file being uploaded.

type subjectId:

string

param subjectId:

[REQUIRED]

The source's subject ID.

type sampleId:

string

param sampleId:

[REQUIRED]

The source's sample ID.

type generatedFrom:

string

param generatedFrom:

Where the source originated.

type referenceArn:

string

param referenceArn:

The ARN of the reference.

type name:

string

param name:

[REQUIRED]

The name of the read set.

type description:

string

param description:

The description of the read set.

type tags:

dict

param tags:

Any tags to add to the read set.

(string) --
- (string) --

rtype:

dict

returns:

Response Syntax

{
    'sequenceStoreId': 'string',
    'uploadId': 'string',
    'sourceFileType': 'FASTQ'|'BAM'|'CRAM'|'UBAM',
    'subjectId': 'string',
    'sampleId': 'string',
    'generatedFrom': 'string',
    'referenceArn': 'string',
    'name': 'string',
    'description': 'string',
    'tags': {
        'string': 'string'
    },
    'creationTime': datetime(2015, 1, 1)
}

Response Structure

(dict) --
- sequenceStoreId (string) --
  
  The sequence store ID for the store that the read set will be created in.
- uploadId (string) --
  
  he ID for the initiated multipart upload.
- sourceFileType (string) --
  
  The file type of the read set source.
- subjectId (string) --
  
  The source's subject ID.
- sampleId (string) --
  
  The source's sample ID.
- generatedFrom (string) --
  
  The source of the read set.
- referenceArn (string) --
  
  The read set source's reference ARN.
- name (string) --
  
  The name of the read set.
- description (string) --
  
  The description of the read set.
- tags (dict) --
  
  The tags to add to the read set.
  - (string) --
    - (string) --
- creationTime (datetime) --
  
  The creation time of the multipart upload.

GetReadSetImportJob (updated)

Link ¶
Changes (response)

{'sources': {'sourceFileType': {'UBAM'}}}

Gets information about a read set import job.

See also: AWS API Documentation

Request Syntax

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

type id:

string

param id:

[REQUIRED]

The job's ID.

type sequenceStoreId:

string

param sequenceStoreId:

[REQUIRED]

The job's sequence store ID.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'sequenceStoreId': 'string',
    'roleArn': 'string',
    'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES',
    'statusMessage': 'string',
    'creationTime': datetime(2015, 1, 1),
    'completionTime': datetime(2015, 1, 1),
    'sources': [
        {
            'sourceFiles': {
                'source1': 'string',
                'source2': 'string'
            },
            'sourceFileType': 'FASTQ'|'BAM'|'CRAM'|'UBAM',
            'status': 'NOT_STARTED'|'IN_PROGRESS'|'FINISHED'|'FAILED',
            'statusMessage': 'string',
            'subjectId': 'string',
            'sampleId': 'string',
            'generatedFrom': 'string',
            'referenceArn': 'string',
            'name': 'string',
            'description': 'string',
            'tags': {
                'string': 'string'
            }
        },
    ]
}

Response Structure

(dict) --
- id (string) --
  
  The job's ID.
- sequenceStoreId (string) --
  
  The job's sequence store ID.
- roleArn (string) --
  
  The job's service role ARN.
- status (string) --
  
  The job's status.
- statusMessage (string) --
  
  The job's status message.
- creationTime (datetime) --
  
  When the job was created.
- completionTime (datetime) --
  
  When the job completed.
- sources (list) --
  
  The job's source files.
  - (dict) --
    
    A source for an import read set job.
    - sourceFiles (dict) --
      
      The source files' location in Amazon S3.
      - source1 (string) --
        
        The location of the first file in Amazon S3.
      - source2 (string) --
        
        The location of the second file in Amazon S3.
    - sourceFileType (string) --
      
      The source's file type.
    - status (string) --
      
      The source's status.
    - statusMessage (string) --
      
      The source's status message.
    - subjectId (string) --
      
      The source's subject ID.
    - sampleId (string) --
      
      The source's sample ID.
    - generatedFrom (string) --
      
      Where the source originated.
    - referenceArn (string) --
      
      The source's genome reference ARN.
    - name (string) --
      
      The source's name.
    - description (string) --
      
      The source's description.
    - tags (dict) --
      
      The source's tags.
      - (string) --
        
        (string) --

GetReadSetMetadata (updated)

Link ¶
Changes (response)

{'fileType': {'UBAM'}}

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
        },
        '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.

ListMultipartReadSetUploads (updated)

Link ¶
Changes (response)

{'uploads': {'sourceFileType': {'UBAM'}}}

Lists all multipart read set uploads and their statuses.

See also: AWS API Documentation

Request Syntax

client.list_multipart_read_set_uploads(
    sequenceStoreId='string',
    maxResults=123,
    nextToken='string'
)

type sequenceStoreId:

string

param sequenceStoreId:

[REQUIRED]

The Sequence Store ID used for the multipart uploads.

type maxResults:

integer

param maxResults:

The maximum number of multipart uploads returned in a page.

type nextToken:

string

param nextToken:

Next token returned in the response of a previous ListMultipartReadSetUploads call. Used to get the next page of results.

rtype:

dict

returns:

Response Syntax

{
    'nextToken': 'string',
    'uploads': [
        {
            'sequenceStoreId': 'string',
            'uploadId': 'string',
            'sourceFileType': 'FASTQ'|'BAM'|'CRAM'|'UBAM',
            'subjectId': 'string',
            'sampleId': 'string',
            'generatedFrom': 'string',
            'referenceArn': 'string',
            'name': 'string',
            'description': 'string',
            'tags': {
                'string': 'string'
            },
            'creationTime': datetime(2015, 1, 1)
        },
    ]
}

Response Structure

(dict) --
- nextToken (string) --
  
  Next token returned in the response of a previous ListMultipartReadSetUploads call. Used to get the next page of results.
- uploads (list) --
  
  An array of multipart uploads.
  - (dict) --
    
    Part of the response to ListMultipartReadSetUploads, excluding completed and aborted multipart uploads.
    - sequenceStoreId (string) --
      
      The sequence store ID used for the multipart upload.
    - uploadId (string) --
      
      The ID for the initiated multipart upload.
    - sourceFileType (string) --
      
      The type of file the read set originated from.
    - subjectId (string) --
      
      The read set source's subject ID.
    - sampleId (string) --
      
      The read set source's sample ID.
    - generatedFrom (string) --
      
      The source of an uploaded part.
    - referenceArn (string) --
      
      The source's reference ARN.
    - name (string) --
      
      The name of a read set.
    - description (string) --
      
      The description of a read set.
    - tags (dict) --
      
      Any tags you wish to add to a read set.
      - (string) --
        
        (string) --
    - creationTime (datetime) --
      
      The time stamp for when a direct upload was created.

ListReadSets (updated)

Link ¶
Changes (response)

{'readSets': {'fileType': {'UBAM'}}}

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',
                '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.

StartReadSetImportJob (updated)

Link ¶
Changes (request)

{'sources': {'sourceFileType': {'UBAM'}}}

Starts a read set import job.

See also: AWS API Documentation

Request Syntax

client.start_read_set_import_job(
    sequenceStoreId='string',
    roleArn='string',
    clientToken='string',
    sources=[
        {
            'sourceFiles': {
                'source1': 'string',
                'source2': 'string'
            },
            'sourceFileType': 'FASTQ'|'BAM'|'CRAM'|'UBAM',
            'subjectId': 'string',
            'sampleId': 'string',
            'generatedFrom': 'string',
            'referenceArn': 'string',
            'name': 'string',
            'description': 'string',
            'tags': {
                'string': 'string'
            }
        },
    ]
)

type sequenceStoreId:

string

param sequenceStoreId:

[REQUIRED]

The read set's sequence store ID.

type roleArn:

string

param roleArn:

[REQUIRED]

A service role for the job.

type clientToken:

string

param clientToken:

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

type sources:

list

param sources:

[REQUIRED]

The job's source files.

(dict) --

A source for a read set import job.
- sourceFiles (dict) -- [REQUIRED]
  
  The source files' location in Amazon S3.
  - source1 (string) -- [REQUIRED]
    
    The location of the first file in Amazon S3.
  - source2 (string) --
    
    The location of the second file in Amazon S3.
- sourceFileType (string) -- [REQUIRED]
  
  The source's file type.
- subjectId (string) -- [REQUIRED]
  
  The source's subject ID.
- sampleId (string) -- [REQUIRED]
  
  The source's sample ID.
- generatedFrom (string) --
  
  Where the source originated.
- referenceArn (string) --
  
  The source's reference ARN.
- name (string) --
  
  The source's name.
- description (string) --
  
  The source's description.
- tags (dict) --
  
  The source's tags.
  - (string) --
    - (string) --

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'sequenceStoreId': 'string',
    'roleArn': 'string',
    'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES',
    'creationTime': datetime(2015, 1, 1)
}

Response Structure

(dict) --
- id (string) --
  
  The job's ID.
- sequenceStoreId (string) --
  
  The read set's sequence store ID.
- roleArn (string) --
  
  The job's service role ARN.
- status (string) --
  
  The job's status.
- creationTime (datetime) --
  
  When the job was created.