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.