Amazon Omics

2024/08/27 - Amazon Omics - 4 updated api methods

Changes  Adds data provenance to import jobs from read sets and references

GetReadSetImportJob (updated) Link ¶
Changes (response)
{'sources': {'readSetId': 'string'}}

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'
            },
            'readSetId': '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) --

        • readSetId (string) --

          The source's read set ID.

GetReadSetMetadata (updated) Link ¶
Changes (response)
{'creationJobId': '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'
    },
    'creationJobId': '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.

    • creationJobId (string) --

      The read set's creation job ID.

GetReferenceImportJob (updated) Link ¶
Changes (response)
{'sources': {'referenceId': 'string'}}

Gets information about a reference import job.

See also: AWS API Documentation

Request Syntax

client.get_reference_import_job(
    id='string',
    referenceStoreId='string'
)
type id

string

param id

[REQUIRED]

The job's ID.

type referenceStoreId

string

param referenceStoreId

[REQUIRED]

The job's reference store ID.

rtype

dict

returns

Response Syntax

{
    'id': 'string',
    'referenceStoreId': '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': [
        {
            'sourceFile': 'string',
            'status': 'NOT_STARTED'|'IN_PROGRESS'|'FINISHED'|'FAILED',
            'statusMessage': 'string',
            'name': 'string',
            'description': 'string',
            'tags': {
                'string': 'string'
            },
            'referenceId': 'string'
        },
    ]
}

Response Structure

  • (dict) --

    • id (string) --

      The job's ID.

    • referenceStoreId (string) --

      The job's reference 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) --

        An genome reference source.

        • sourceFile (string) --

          The source file's location in Amazon S3.

        • status (string) --

          The source's status.

        • statusMessage (string) --

          The source's status message.

        • name (string) --

          The source's name.

        • description (string) --

          The source's description.

        • tags (dict) --

          The source's tags.

          • (string) --

            • (string) --

        • referenceId (string) --

          The source's reference ID.

GetReferenceMetadata (updated) Link ¶
Changes (response)
{'creationJobId': 'string', 'creationType': 'IMPORT'}

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'
            }
        }
    },
    'creationType': 'IMPORT',
    'creationJobId': '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.

    • creationType (string) --

      The reference's creation type.

    • creationJobId (string) --

      The reference's creation job ID.