2024/08/27 - Amazon Omics - 4 updated api methods
Changes Adds data provenance to import jobs from read sets and references
{'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'
)
string
[REQUIRED]
The job's ID.
string
[REQUIRED]
The job's sequence store ID.
dict
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.
{'creationJobId': 'string'}
Gets details about a read set.
See also: AWS API Documentation
Request Syntax
client.get_read_set_metadata(
id='string',
sequenceStoreId='string'
)
string
[REQUIRED]
The read set's ID.
string
[REQUIRED]
The read set's sequence store ID.
dict
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.
{'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'
)
string
[REQUIRED]
The job's ID.
string
[REQUIRED]
The job's reference store ID.
dict
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.
{'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'
)
string
[REQUIRED]
The reference's ID.
string
[REQUIRED]
The reference's reference store ID.
dict
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.