2023/05/11 - Amazon Omics - 6 new23 updated api methods
Changes This release provides support for Ready2Run and GPU workflows, an improved read set filter, the direct upload of read sets into Omics Storage, and annotation parsing for analytics stores.
Concludes a multipart upload once you have uploaded all the components.
See also: AWS API Documentation
Request Syntax
client.complete_multipart_read_set_upload(
sequenceStoreId='string',
uploadId='string',
parts=[
{
'partNumber': 123,
'partSource': 'SOURCE1'|'SOURCE2',
'checksum': 'string'
},
]
)
string
[REQUIRED]
The sequence store ID for the store involved in the multipart upload.
string
[REQUIRED]
The ID for the multipart upload.
list
[REQUIRED]
The individual uploads or parts of a multipart upload.
(dict) --
Part of the response to the CompleteReadSetUpload API, including metadata.
partNumber (integer) -- [REQUIRED]
A number identifying the part in a read set upload.
partSource (string) -- [REQUIRED]
The source file of the part being uploaded.
checksum (string) -- [REQUIRED]
A unique identifier used to confirm that parts are being added to the correct upload.
dict
Response Syntax
{
'readSetId': 'string'
}
Response Structure
(dict) --
readSetId (string) --
The read set ID created for an uploaded read set.
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',
subjectId='string',
sampleId='string',
generatedFrom='string',
referenceArn='string',
name='string',
description='string',
tags={
'string': 'string'
}
)
string
[REQUIRED]
The sequence store ID for the store that is the destination of the multipart uploads.
string
An idempotency token that can be used to avoid triggering multiple multipart uploads.
string
[REQUIRED]
The type of file being uploaded.
string
[REQUIRED]
The source's subject ID.
string
[REQUIRED]
The source's sample ID.
string
Where the source originated.
string
[REQUIRED]
The ARN of the reference.
string
[REQUIRED]
The name of the read set.
string
The description of the read set.
dict
Any tags to add to the read set.
(string) --
(string) --
dict
Response Syntax
{
'sequenceStoreId': 'string',
'uploadId': 'string',
'sourceFileType': 'FASTQ'|'BAM'|'CRAM',
'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.
Stops a multipart upload.
See also: AWS API Documentation
Request Syntax
client.abort_multipart_read_set_upload(
sequenceStoreId='string',
uploadId='string'
)
string
[REQUIRED]
The sequence store ID for the store involved in the multipart upload.
string
[REQUIRED]
The ID for the multipart upload.
dict
Response Syntax
{}
Response Structure
(dict) --
This operation will list all parts in a requested multipart upload for a sequence store.
See also: AWS API Documentation
Request Syntax
client.list_read_set_upload_parts(
sequenceStoreId='string',
uploadId='string',
partSource='SOURCE1'|'SOURCE2',
maxResults=123,
nextToken='string',
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1)
}
)
string
[REQUIRED]
The Sequence Store ID used for the multipart uploads.
string
[REQUIRED]
The ID for the initiated multipart upload.
string
[REQUIRED]
The source file for the upload part.
integer
The maximum number of read set upload parts returned in a page.
string
Next token returned in the response of a previous ListReadSetUploadPartsRequest call. Used to get the next page of results.
dict
Attributes used to filter for a specific subset of read set part uploads.
createdAfter (datetime) --
Filters for read set uploads after a specified time.
createdBefore (datetime) --
Filters for read set part uploads before a specified time.
dict
Response Syntax
{
'nextToken': 'string',
'parts': [
{
'partNumber': 123,
'partSize': 123,
'partSource': 'SOURCE1'|'SOURCE2',
'checksum': 'string',
'creationTime': datetime(2015, 1, 1),
'lastUpdatedTime': datetime(2015, 1, 1)
},
]
}
Response Structure
(dict) --
nextToken (string) --
Next token returned in the response of a previous ListReadSetUploadParts call. Used to get the next page of results.
parts (list) --
An array of upload parts.
(dict) --
The metadata of a single part of a file that was added to a multipart upload. A list of these parts is returned in the response to the ListReadSetUploadParts API.
partNumber (integer) --
The number identifying the part in an upload.
partSize (integer) --
The size of the the part in an upload.
partSource (string) --
The origin of the part being direct uploaded.
checksum (string) --
A unique identifier used to confirm that parts are being added to the correct upload.
creationTime (datetime) --
The time stamp for when a direct upload was created.
lastUpdatedTime (datetime) --
The time stamp for the most recent update to an uploaded part.
This operation uploads a specific part of a read set. If you upload a new part using a previously used part number, the previously uploaded part will be overwritten.
See also: AWS API Documentation
Request Syntax
client.upload_read_set_part(
sequenceStoreId='string',
uploadId='string',
partSource='SOURCE1'|'SOURCE2',
partNumber=123,
payload=b'bytes'|file
)
string
[REQUIRED]
The Sequence Store ID used for the multipart upload.
string
[REQUIRED]
The ID for the initiated multipart upload.
string
[REQUIRED]
The source file for an upload part.
integer
[REQUIRED]
The number of the part being uploaded.
bytes or seekable file-like object
[REQUIRED]
The read set data to upload for a part.
dict
Response Syntax
{
'checksum': 'string'
}
Response Structure
(dict) --
checksum (string) --
An identifier used to confirm that parts are being added to the intended upload.
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'
)
string
[REQUIRED]
The Sequence Store ID used for the multipart uploads.
integer
The maximum number of multipart uploads returned in a page.
string
Next token returned in the response of a previous ListMultipartReadSetUploads call. Used to get the next page of results.
dict
Response Syntax
{
'nextToken': 'string',
'uploads': [
{
'sequenceStoreId': 'string',
'uploadId': 'string',
'sourceFileType': 'FASTQ'|'BAM'|'CRAM',
'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.
{'maxGpus': 'integer'}
Creates a run group.
See also: AWS API Documentation
Request Syntax
client.create_run_group(
name='string',
maxCpus=123,
maxRuns=123,
maxDuration=123,
tags={
'string': 'string'
},
requestId='string',
maxGpus=123
)
string
A name for the group.
integer
The maximum number of CPUs to use in the group.
integer
The maximum number of concurrent runs for the group.
integer
A maximum run time for the group in minutes.
dict
Tags for the group.
(string) --
(string) --
string
[REQUIRED]
To ensure that requests don't run multiple times, specify a unique ID for each request.
This field is autopopulated if not provided.
integer
The maximum GPUs that can be used by a run group.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'tags': {
'string': 'string'
}
}
Response Structure
(dict) --
arn (string) --
The group's ARN.
id (string) --
The group's ID.
tags (dict) --
Tags for the run group.
(string) --
(string) --
{'fallbackLocation': 'string'}
Creates a sequence store.
See also: AWS API Documentation
Request Syntax
client.create_sequence_store(
name='string',
description='string',
sseConfig={
'type': 'KMS',
'keyArn': 'string'
},
tags={
'string': 'string'
},
clientToken='string',
fallbackLocation='string'
)
string
[REQUIRED]
A name for the store.
string
A description for the store.
dict
Server-side encryption (SSE) settings for the store.
type (string) -- [REQUIRED]
The encryption type.
keyArn (string) --
An encryption key ARN.
dict
Tags for the store.
(string) --
(string) --
string
To ensure that requests don't run multiple times, specify a unique token for each request.
string
An S3 location that is used to store files that have failed a direct upload.
dict
Response Syntax
{
'id': 'string',
'arn': 'string',
'name': 'string',
'description': 'string',
'sseConfig': {
'type': 'KMS',
'keyArn': 'string'
},
'creationTime': datetime(2015, 1, 1),
'fallbackLocation': 'string'
}
Response Structure
(dict) --
id (string) --
The store's ID.
arn (string) --
The store's ARN.
name (string) --
The store's name.
description (string) --
The store's description.
sseConfig (dict) --
The store's SSE settings.
type (string) --
The encryption type.
keyArn (string) --
An encryption key ARN.
creationTime (datetime) --
When the store was created.
fallbackLocation (string) --
An S3 location that is used to store files that have failed a direct upload.
{'accelerators': 'GPU'}
Response {'status': {'INACTIVE'}}
Creates a workflow.
See also: AWS API Documentation
Request Syntax
client.create_workflow(
name='string',
description='string',
engine='WDL'|'NEXTFLOW',
definitionZip=b'bytes',
definitionUri='string',
main='string',
parameterTemplate={
'string': {
'description': 'string',
'optional': True|False
}
},
storageCapacity=123,
tags={
'string': 'string'
},
requestId='string',
accelerators='GPU'
)
string
A name for the workflow.
string
A description for the workflow.
string
An engine for the workflow.
bytes
A ZIP archive for the workflow.
string
The URI of a definition for the workflow.
string
The path of the main definition file for the workflow.
dict
A parameter template for the workflow.
(string) --
(dict) --
A workflow parameter.
description (string) --
The parameter's description.
optional (boolean) --
Whether the parameter is optional.
integer
A storage capacity for the workflow in gigabytes.
dict
Tags for the workflow.
(string) --
(string) --
string
[REQUIRED]
To ensure that requests don't run multiple times, specify a unique ID for each request.
This field is autopopulated if not provided.
string
The computational accelerator specified to run the workflow.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
'tags': {
'string': 'string'
}
}
Response Structure
(dict) --
arn (string) --
The workflow's ARN.
id (string) --
The workflow's ID.
status (string) --
The workflow's status.
tags (dict) --
The workflow's tags.
(string) --
(string) --
{'annotationFields': {'string': 'string'}}
Gets information about an annotation import job.
See also: AWS API Documentation
Request Syntax
client.get_annotation_import_job(
jobId='string'
)
string
[REQUIRED]
The job's ID.
dict
Response Syntax
{
'id': 'string',
'destinationName': 'string',
'roleArn': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
'statusMessage': 'string',
'creationTime': datetime(2015, 1, 1),
'updateTime': datetime(2015, 1, 1),
'completionTime': datetime(2015, 1, 1),
'items': [
{
'source': 'string',
'jobStatus': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES'
},
],
'runLeftNormalization': True|False,
'formatOptions': {
'tsvOptions': {
'readOptions': {
'sep': 'string',
'encoding': 'string',
'quote': 'string',
'quoteAll': True|False,
'escape': 'string',
'escapeQuotes': True|False,
'comment': 'string',
'header': True|False,
'lineSep': 'string'
}
},
'vcfOptions': {
'ignoreQualField': True|False,
'ignoreFilterField': True|False
}
},
'annotationFields': {
'string': 'string'
}
}
Response Structure
(dict) --
id (string) --
The job's ID.
destinationName (string) --
The job's destination annotation store.
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.
updateTime (datetime) --
When the job was updated.
completionTime (datetime) --
When the job completed.
items (list) --
The job's imported items.
(dict) --
Details about an imported annotation item.
source (string) --
The source file's location in Amazon S3.
jobStatus (string) --
The item's job status.
runLeftNormalization (boolean) --
The job's left normalization setting.
formatOptions (dict) --
Formatting options for a file.
tsvOptions (dict) --
Options for a TSV file.
readOptions (dict) --
The file's read options.
sep (string) --
The file's field separator.
encoding (string) --
The file's encoding.
quote (string) --
The file's quote character.
quoteAll (boolean) --
Whether all values need to be quoted, or just those that contain quotes.
escape (string) --
A character for escaping quotes in the file.
escapeQuotes (boolean) --
Whether quotes need to be escaped in the file.
comment (string) --
The file's comment character.
header (boolean) --
Whether the file has a header row.
lineSep (string) --
A line separator for the file.
vcfOptions (dict) --
Options for a VCF file.
ignoreQualField (boolean) --
The file's ignore qual field setting.
ignoreFilterField (boolean) --
The file's ignore filter field setting.
annotationFields (dict) --
The annotation schema generated by the parsed annotation data.
(string) --
(string) --
{'status': {'PROCESSING_UPLOAD', 'UPLOAD_FAILED'}, 'statusMessage': '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',
'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'
}
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.
{'accelerators': 'GPU', 'workflowType': {'READY2RUN'}}
Gets information about a workflow run.
See also: AWS API Documentation
Request Syntax
client.get_run(
id='string',
export=[
'DEFINITION',
]
)
string
[REQUIRED]
The run's ID.
list
The run's export format.
(string) --
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED',
'workflowId': 'string',
'workflowType': 'PRIVATE'|'READY2RUN',
'runId': 'string',
'roleArn': 'string',
'name': 'string',
'runGroupId': 'string',
'priority': 123,
'definition': 'string',
'digest': 'string',
'parameters': {...}|[...]|123|123.4|'string'|True|None,
'storageCapacity': 123,
'outputUri': 'string',
'logLevel': 'OFF'|'FATAL'|'ERROR'|'ALL',
'resourceDigests': {
'string': 'string'
},
'startedBy': 'string',
'creationTime': datetime(2015, 1, 1),
'startTime': datetime(2015, 1, 1),
'stopTime': datetime(2015, 1, 1),
'statusMessage': 'string',
'tags': {
'string': 'string'
},
'accelerators': 'GPU'
}
Response Structure
(dict) --
arn (string) --
The run's ARN.
id (string) --
The run's ID.
status (string) --
The run's status.
workflowId (string) --
The run's workflow ID.
workflowType (string) --
The run's workflow type.
runId (string) --
The run's ID.
roleArn (string) --
The run's service role ARN.
name (string) --
The run's name.
runGroupId (string) --
The run's group ID.
priority (integer) --
The run's priority.
definition (string) --
The run's definition.
digest (string) --
The run's digest.
parameters (:ref:`document<document>`) --
The run's parameters.
storageCapacity (integer) --
The run's storage capacity in gigabytes.
outputUri (string) --
The run's output URI.
logLevel (string) --
The run's log level.
resourceDigests (dict) --
The run's resource digests.
(string) --
(string) --
startedBy (string) --
Who started the run.
creationTime (datetime) --
When the run was created.
startTime (datetime) --
When the run started.
stopTime (datetime) --
The run's stop time.
statusMessage (string) --
The run's status message.
tags (dict) --
The run's tags.
(string) --
(string) --
accelerators (string) --
The computational accelerator used to run the workflow.
{'maxGpus': 'integer'}
Gets information about a workflow run group.
See also: AWS API Documentation
Request Syntax
client.get_run_group(
id='string'
)
string
[REQUIRED]
The group's ID.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'name': 'string',
'maxCpus': 123,
'maxRuns': 123,
'maxDuration': 123,
'creationTime': datetime(2015, 1, 1),
'tags': {
'string': 'string'
},
'maxGpus': 123
}
Response Structure
(dict) --
arn (string) --
The group's ARN.
id (string) --
The group's ID.
name (string) --
The group's name.
maxCpus (integer) --
The group's maximum number of CPUs to use.
maxRuns (integer) --
The maximum number of concurrent runs for the group.
maxDuration (integer) --
The group's maximum run time in minutes.
creationTime (datetime) --
When the group was created.
tags (dict) --
The group's tags.
(string) --
(string) --
maxGpus (integer) --
The maximum GPUs that can be used by a run group.
{'gpus': 'integer'}
Gets information about a workflow run task.
See also: AWS API Documentation
Request Syntax
client.get_run_task(
id='string',
taskId='string'
)
string
[REQUIRED]
The task's ID.
string
[REQUIRED]
The task's ID.
dict
Response Syntax
{
'taskId': 'string',
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED',
'name': 'string',
'cpus': 123,
'memory': 123,
'creationTime': datetime(2015, 1, 1),
'startTime': datetime(2015, 1, 1),
'stopTime': datetime(2015, 1, 1),
'statusMessage': 'string',
'logStream': 'string',
'gpus': 123
}
Response Structure
(dict) --
taskId (string) --
The task's ID.
status (string) --
The task's status.
name (string) --
The task's name.
cpus (integer) --
The task's CPU usage.
memory (integer) --
The task's memory use in gigabytes.
creationTime (datetime) --
When the task was created.
startTime (datetime) --
The task's start time.
stopTime (datetime) --
The task's stop time.
statusMessage (string) --
The task's status message.
logStream (string) --
The task's log stream.
gpus (integer) --
The number of Graphics Processing Units (GPU) specified in the task.
{'fallbackLocation': 'string'}
Gets information about a sequence store.
See also: AWS API Documentation
Request Syntax
client.get_sequence_store(
id='string'
)
string
[REQUIRED]
The store's ID.
dict
Response Syntax
{
'id': 'string',
'arn': 'string',
'name': 'string',
'description': 'string',
'sseConfig': {
'type': 'KMS',
'keyArn': 'string'
},
'creationTime': datetime(2015, 1, 1),
'fallbackLocation': 'string'
}
Response Structure
(dict) --
id (string) --
The store's ID.
arn (string) --
The store's ARN.
name (string) --
The store's name.
description (string) --
The store's description.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
type (string) --
The encryption type.
keyArn (string) --
An encryption key ARN.
creationTime (datetime) --
When the store was created.
fallbackLocation (string) --
An S3 location that is used to store files that have failed a direct upload.
{'annotationFields': {'string': 'string'}}
Gets information about a variant import job.
See also: AWS API Documentation
Request Syntax
client.get_variant_import_job(
jobId='string'
)
string
[REQUIRED]
The job's ID.
dict
Response Syntax
{
'id': 'string',
'destinationName': 'string',
'roleArn': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
'statusMessage': 'string',
'creationTime': datetime(2015, 1, 1),
'updateTime': datetime(2015, 1, 1),
'completionTime': datetime(2015, 1, 1),
'items': [
{
'source': 'string',
'jobStatus': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
'statusMessage': 'string'
},
],
'runLeftNormalization': True|False,
'annotationFields': {
'string': 'string'
}
}
Response Structure
(dict) --
id (string) --
The job's ID.
destinationName (string) --
The job's destination variant store.
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.
updateTime (datetime) --
When the job was updated.
completionTime (datetime) --
When the job completed.
items (list) --
The job's items.
(dict) --
Details about an imported variant item.
source (string) --
The source file's location in Amazon S3.
jobStatus (string) --
The item's job status.
statusMessage (string) --
A message that provides additional context about a job
runLeftNormalization (boolean) --
The job's left normalization setting.
annotationFields (dict) --
The annotation schema generated by the parsed annotation data.
(string) --
(string) --
{'type': {'READY2RUN'}}
Response {'accelerators': 'GPU',
'metadata': {'string': 'string'},
'status': {'INACTIVE'},
'type': {'READY2RUN'}}
Gets information about a workflow.
See also: AWS API Documentation
Request Syntax
client.get_workflow(
id='string',
type='PRIVATE'|'READY2RUN',
export=[
'DEFINITION',
]
)
string
[REQUIRED]
The workflow's ID.
string
The workflow's type.
list
The export format for the workflow.
(string) --
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
'type': 'PRIVATE'|'READY2RUN',
'name': 'string',
'description': 'string',
'engine': 'WDL'|'NEXTFLOW',
'definition': 'string',
'main': 'string',
'digest': 'string',
'parameterTemplate': {
'string': {
'description': 'string',
'optional': True|False
}
},
'storageCapacity': 123,
'creationTime': datetime(2015, 1, 1),
'statusMessage': 'string',
'tags': {
'string': 'string'
},
'metadata': {
'string': 'string'
},
'accelerators': 'GPU'
}
Response Structure
(dict) --
arn (string) --
The workflow's ARN.
id (string) --
The workflow's ID.
status (string) --
The workflow's status.
type (string) --
The workflow's type.
name (string) --
The workflow's name.
description (string) --
The workflow's description.
engine (string) --
The workflow's engine.
definition (string) --
The workflow's definition.
main (string) --
The path of the main definition file for the workflow.
digest (string) --
The workflow's digest.
parameterTemplate (dict) --
The workflow's parameter template.
(string) --
(dict) --
A workflow parameter.
description (string) --
The parameter's description.
optional (boolean) --
Whether the parameter is optional.
storageCapacity (integer) --
The workflow's storage capacity in gigabytes.
creationTime (datetime) --
When the workflow was created.
statusMessage (string) --
The workflow's status message.
tags (dict) --
The workflow's tags.
(string) --
(string) --
metadata (dict) --
Gets metadata for workflow.
(string) --
(string) --
accelerators (string) --
The computational accelerator specified to run the workflow.
{'annotationImportJobs': {'annotationFields': {'string': 'string'}}}
Retrieves a list of annotation import jobs.
See also: AWS API Documentation
Request Syntax
client.list_annotation_import_jobs(
maxResults=123,
ids=[
'string',
],
nextToken='string',
filter={
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
'storeName': 'string'
}
)
integer
The maximum number of jobs to return in one page of results.
list
IDs of annotation import jobs to retrieve.
(string) --
string
Specify the pagination token from a previous request to retrieve the next page of results.
dict
A filter to apply to the list.
status (string) --
A status to filter on.
storeName (string) --
A store name to filter on.
dict
Response Syntax
{
'annotationImportJobs': [
{
'id': 'string',
'destinationName': 'string',
'roleArn': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
'creationTime': datetime(2015, 1, 1),
'updateTime': datetime(2015, 1, 1),
'completionTime': datetime(2015, 1, 1),
'runLeftNormalization': True|False,
'annotationFields': {
'string': 'string'
}
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
annotationImportJobs (list) --
A list of jobs.
(dict) --
An annotation import job.
id (string) --
The job's ID.
destinationName (string) --
The job's destination annotation store.
roleArn (string) --
The job's service role ARN.
status (string) --
The job's status.
creationTime (datetime) --
When the job was created.
updateTime (datetime) --
When the job was updated.
completionTime (datetime) --
When the job completed.
runLeftNormalization (boolean) --
The job's left normalization setting.
annotationFields (dict) --
The annotation schema generated by the parsed annotation data.
(string) --
(string) --
nextToken (string) --
A pagination token that's included if more results are available.
{'filter': {'generatedFrom': 'string',
'sampleId': 'string',
'status': {'PROCESSING_UPLOAD', 'UPLOAD_FAILED'},
'subjectId': 'string'}}
Response {'readSets': {'status': {'PROCESSING_UPLOAD', 'UPLOAD_FAILED'},
'statusMessage': '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'
}
)
string
[REQUIRED]
The jobs' sequence store ID.
integer
The maximum number of read sets to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
dict
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.
dict
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'
},
]
}
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.
{'items': {'maxGpus': 'integer'}}
Retrieves a list of run groups.
See also: AWS API Documentation
Request Syntax
client.list_run_groups(
name='string',
startingToken='string',
maxResults=123
)
string
The run groups' name.
string
Specify the pagination token from a previous request to retrieve the next page of results.
integer
The maximum number of run groups to return in one page of results.
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'id': 'string',
'name': 'string',
'maxCpus': 123,
'maxRuns': 123,
'maxDuration': 123,
'creationTime': datetime(2015, 1, 1),
'maxGpus': 123
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of groups.
(dict) --
A run group.
arn (string) --
The group's ARN.
id (string) --
The group's ID.
name (string) --
The group's name.
maxCpus (integer) --
The group's maximum CPU count setting.
maxRuns (integer) --
The group's maximum concurrent run setting.
maxDuration (integer) --
The group's maximum duration setting in minutes.
creationTime (datetime) --
When the group was created.
maxGpus (integer) --
The maximum GPUs that can be used by a run group.
nextToken (string) --
A pagination token that's included if more results are available.
{'items': {'gpus': 'integer'}}
Retrieves a list of tasks for a run.
See also: AWS API Documentation
Request Syntax
client.list_run_tasks(
id='string',
status='PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED',
startingToken='string',
maxResults=123
)
string
[REQUIRED]
The run's ID.
string
Filter the list by status.
string
Specify the pagination token from a previous request to retrieve the next page of results.
integer
The maximum number of run tasks to return in one page of results.
dict
Response Syntax
{
'items': [
{
'taskId': 'string',
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED',
'name': 'string',
'cpus': 123,
'memory': 123,
'creationTime': datetime(2015, 1, 1),
'startTime': datetime(2015, 1, 1),
'stopTime': datetime(2015, 1, 1),
'gpus': 123
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of tasks.
(dict) --
A workflow run task.
taskId (string) --
The task's ID.
status (string) --
The task's status.
name (string) --
The task's name.
cpus (integer) --
The task's CPU count.
memory (integer) --
The task's memory use in gigabyes.
creationTime (datetime) --
When the task was created.
startTime (datetime) --
When the task started.
stopTime (datetime) --
When the task stopped.
gpus (integer) --
The number of Graphics Processing Units (GPU) specified for the task.
nextToken (string) --
A pagination token that's included if more results are available.
{'status': 'PENDING | STARTING | RUNNING | STOPPING | COMPLETED | DELETED | '
'CANCELLED | FAILED'}
Retrieves a list of runs.
See also: AWS API Documentation
Request Syntax
client.list_runs(
name='string',
runGroupId='string',
startingToken='string',
maxResults=123,
status='PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED'
)
string
Filter the list by run name.
string
Filter the list by run group ID.
string
Specify the pagination token from a previous request to retrieve the next page of results.
integer
The maximum number of runs to return in one page of results.
string
The status of a run.
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'id': 'string',
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED',
'workflowId': 'string',
'name': 'string',
'priority': 123,
'storageCapacity': 123,
'creationTime': datetime(2015, 1, 1),
'startTime': datetime(2015, 1, 1),
'stopTime': datetime(2015, 1, 1)
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of runs.
(dict) --
A workflow run.
arn (string) --
The run's ARN.
id (string) --
The run's ID.
status (string) --
The run's status.
workflowId (string) --
The run's workflow ID.
name (string) --
The run's name.
priority (integer) --
The run's priority.
storageCapacity (integer) --
The run's storage capacity.
creationTime (datetime) --
When the run was created.
startTime (datetime) --
When the run started.
stopTime (datetime) --
When the run stopped.
nextToken (string) --
A pagination token that's included if more results are available.
{'sequenceStores': {'fallbackLocation': 'string'}}
Retrieves a list of sequence stores.
See also: AWS API Documentation
Request Syntax
client.list_sequence_stores(
maxResults=123,
nextToken='string',
filter={
'name': 'string',
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1)
}
)
integer
The maximum number of stores to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
dict
A filter to apply to the list.
name (string) --
A name to filter on.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
dict
Response Syntax
{
'nextToken': 'string',
'sequenceStores': [
{
'arn': 'string',
'id': 'string',
'name': 'string',
'description': 'string',
'sseConfig': {
'type': 'KMS',
'keyArn': 'string'
},
'creationTime': datetime(2015, 1, 1),
'fallbackLocation': 'string'
},
]
}
Response Structure
(dict) --
nextToken (string) --
A pagination token that's included if more results are available.
sequenceStores (list) --
A list of sequence stores.
(dict) --
Details about a sequence store.
arn (string) --
The store's ARN.
id (string) --
The store's ID.
name (string) --
The store's name.
description (string) --
The store's description.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
type (string) --
The encryption type.
keyArn (string) --
An encryption key ARN.
creationTime (datetime) --
When the store was created.
fallbackLocation (string) --
An S3 location that is used to store files that have failed a direct upload.
{'variantImportJobs': {'annotationFields': {'string': 'string'}}}
Retrieves a list of variant import jobs.
See also: AWS API Documentation
Request Syntax
client.list_variant_import_jobs(
maxResults=123,
ids=[
'string',
],
nextToken='string',
filter={
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
'storeName': 'string'
}
)
integer
The maximum number of import jobs to return in one page of results.
list
A list of job IDs.
(string) --
string
Specify the pagination token from a previous request to retrieve the next page of results.
dict
A filter to apply to the list.
status (string) --
A status to filter on.
storeName (string) --
A store name to filter on.
dict
Response Syntax
{
'variantImportJobs': [
{
'id': 'string',
'destinationName': 'string',
'roleArn': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
'creationTime': datetime(2015, 1, 1),
'updateTime': datetime(2015, 1, 1),
'completionTime': datetime(2015, 1, 1),
'runLeftNormalization': True|False,
'annotationFields': {
'string': 'string'
}
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
variantImportJobs (list) --
A list of jobs.
(dict) --
A variant import job.
id (string) --
The job's ID.
destinationName (string) --
The job's destination variant store.
roleArn (string) --
The job's service role ARN.
status (string) --
The job's status.
creationTime (datetime) --
When the job was created.
updateTime (datetime) --
When the job was updated.
completionTime (datetime) --
When the job completed.
runLeftNormalization (boolean) --
The job's left normalization setting.
annotationFields (dict) --
The annotation schema generated by the parsed annotation data.
(string) --
(string) --
nextToken (string) --
A pagination token that's included if more results are available.
{'type': {'READY2RUN'}}
Response {'items': {'metadata': {'string': 'string'},
'status': {'INACTIVE'},
'type': {'READY2RUN'}}}
Retrieves a list of workflows.
See also: AWS API Documentation
Request Syntax
client.list_workflows(
type='PRIVATE'|'READY2RUN',
name='string',
startingToken='string',
maxResults=123
)
string
The workflows' type.
string
The workflows' name.
string
Specify the pagination token from a previous request to retrieve the next page of results.
integer
The maximum number of workflows to return in one page of results.
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'id': 'string',
'name': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
'type': 'PRIVATE'|'READY2RUN',
'digest': 'string',
'creationTime': datetime(2015, 1, 1),
'metadata': {
'string': 'string'
}
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
items (list) --
The workflows' items.
(dict) --
A workflow.
arn (string) --
The workflow's ARN.
id (string) --
The workflow's ID.
name (string) --
The workflow's name.
status (string) --
The workflow's status.
type (string) --
The workflow's type.
digest (string) --
The workflow's digest.
creationTime (datetime) --
When the workflow was created.
metadata (dict) --
Any metadata available for workflow. The information listed may vary depending on the workflow, and there may also be no metadata to return.
(string) --
(string) --
nextToken (string) --
A pagination token that's included if more results are available.
{'annotationFields': {'string': 'string'}}
Starts an annotation import job.
See also: AWS API Documentation
Request Syntax
client.start_annotation_import_job(
destinationName='string',
roleArn='string',
items=[
{
'source': 'string'
},
],
formatOptions={
'tsvOptions': {
'readOptions': {
'sep': 'string',
'encoding': 'string',
'quote': 'string',
'quoteAll': True|False,
'escape': 'string',
'escapeQuotes': True|False,
'comment': 'string',
'header': True|False,
'lineSep': 'string'
}
},
'vcfOptions': {
'ignoreQualField': True|False,
'ignoreFilterField': True|False
}
},
runLeftNormalization=True|False,
annotationFields={
'string': 'string'
}
)
string
[REQUIRED]
A destination annotation store for the job.
string
[REQUIRED]
A service role for the job.
list
[REQUIRED]
Items to import.
(dict) --
A source for an annotation import job.
source (string) -- [REQUIRED]
The source file's location in Amazon S3.
dict
Formatting options for the annotation file.
tsvOptions (dict) --
Options for a TSV file.
readOptions (dict) --
The file's read options.
sep (string) --
The file's field separator.
encoding (string) --
The file's encoding.
quote (string) --
The file's quote character.
quoteAll (boolean) --
Whether all values need to be quoted, or just those that contain quotes.
escape (string) --
A character for escaping quotes in the file.
escapeQuotes (boolean) --
Whether quotes need to be escaped in the file.
comment (string) --
The file's comment character.
header (boolean) --
Whether the file has a header row.
lineSep (string) --
A line separator for the file.
vcfOptions (dict) --
Options for a VCF file.
ignoreQualField (boolean) --
The file's ignore qual field setting.
ignoreFilterField (boolean) --
The file's ignore filter field setting.
boolean
The job's left normalization setting.
dict
The annotation schema generated by the parsed annotation data.
(string) --
(string) --
dict
Response Syntax
{
'jobId': 'string'
}
Response Structure
(dict) --
jobId (string) --
The job's ID.
{'workflowType': {'READY2RUN'}}
Starts a run.
See also: AWS API Documentation
Request Syntax
client.start_run(
workflowId='string',
workflowType='PRIVATE'|'READY2RUN',
runId='string',
roleArn='string',
name='string',
runGroupId='string',
priority=123,
parameters={...}|[...]|123|123.4|'string'|True|None,
storageCapacity=123,
outputUri='string',
logLevel='OFF'|'FATAL'|'ERROR'|'ALL',
tags={
'string': 'string'
},
requestId='string'
)
string
The run's workflow ID.
string
The run's workflows type.
string
The run's ID.
string
[REQUIRED]
A service role for the run.
string
A name for the run.
string
The run's group ID.
integer
A priority for the run.
:ref:`document<document>`
Parameters for the run.
integer
A storage capacity for the run in gigabytes.
string
An output URI for the run.
string
A log level for the run.
dict
Tags for the run.
(string) --
(string) --
string
[REQUIRED]
To ensure that requests don't run multiple times, specify a unique ID for each request.
This field is autopopulated if not provided.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED',
'tags': {
'string': 'string'
}
}
Response Structure
(dict) --
arn (string) --
The run's ARN.
id (string) --
The run's ID.
status (string) --
The run's status.
tags (dict) --
The run's tags.
(string) --
(string) --
{'annotationFields': {'string': 'string'}}
Starts a variant import job.
See also: AWS API Documentation
Request Syntax
client.start_variant_import_job(
destinationName='string',
roleArn='string',
items=[
{
'source': 'string'
},
],
runLeftNormalization=True|False,
annotationFields={
'string': 'string'
}
)
string
[REQUIRED]
The destination variant store for the job.
string
[REQUIRED]
A service role for the job.
list
[REQUIRED]
Items to import.
(dict) --
A imported variant item's source.
source (string) -- [REQUIRED]
The source file's location in Amazon S3.
boolean
The job's left normalization setting.
dict
The annotation schema generated by the parsed annotation data.
(string) --
(string) --
dict
Response Syntax
{
'jobId': 'string'
}
Response Structure
(dict) --
jobId (string) --
The job's ID.
{'maxGpus': 'integer'}
Updates a run group.
See also: AWS API Documentation
Request Syntax
client.update_run_group(
id='string',
name='string',
maxCpus=123,
maxRuns=123,
maxDuration=123,
maxGpus=123
)
string
[REQUIRED]
The group's ID.
string
A name for the group.
integer
The maximum number of CPUs to use.
integer
The maximum number of concurrent runs for the group.
integer
A maximum run time for the group in minutes.
integer
The maximum GPUs that can be used by a run group.
None