Amazon Omics

2026/04/27 - Amazon Omics - 3 updated api methods

Changes  Enable Public Internet or VPC configuration to BatchRun

GetBatch (updated) Link ¶
Changes (response) 
{'defaultRunSetting': {'configurationName': 'string',
                       'networkingMode': 'RESTRICTED | VPC'},
 'status': {'CREATING'}}

Retrieves details and current status for a specific run batch, including submission progress and run execution counts.

See also: AWS API Documentation

Request Syntax

client.get_batch(
    batchId='string'
)
type batchId:

string

param batchId:

[REQUIRED]

The identifier portion of the run batch ARN.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'arn': 'string',
    'uuid': 'string',
    'name': 'string',
    'status': 'CREATING'|'PENDING'|'SUBMITTING'|'INPROGRESS'|'STOPPING'|'CANCELLED'|'FAILED'|'PROCESSED'|'RUNS_DELETING'|'RUNS_DELETED',
    'tags': {
        'string': 'string'
    },
    'totalRuns': 123,
    'defaultRunSetting': {
        'workflowId': 'string',
        'workflowType': 'PRIVATE'|'READY2RUN',
        'roleArn': 'string',
        'name': 'string',
        'cacheId': 'string',
        'cacheBehavior': 'CACHE_ON_FAILURE'|'CACHE_ALWAYS',
        'runGroupId': 'string',
        'priority': 123,
        'parameters': {...}|[...]|123|123.4|'string'|True|None,
        'storageCapacity': 123,
        'outputUri': 'string',
        'logLevel': 'OFF'|'FATAL'|'ERROR'|'ALL',
        'runTags': {
            'string': 'string'
        },
        'retentionMode': 'RETAIN'|'REMOVE',
        'storageType': 'STATIC'|'DYNAMIC',
        'workflowOwnerId': 'string',
        'outputBucketOwnerId': 'string',
        'workflowVersionName': 'string',
        'networkingMode': 'RESTRICTED'|'VPC',
        'configurationName': 'string'
    },
    'submissionSummary': {
        'successfulStartSubmissionCount': 123,
        'failedStartSubmissionCount': 123,
        'pendingStartSubmissionCount': 123,
        'successfulCancelSubmissionCount': 123,
        'failedCancelSubmissionCount': 123,
        'successfulDeleteSubmissionCount': 123,
        'failedDeleteSubmissionCount': 123
    },
    'runSummary': {
        'pendingRunCount': 123,
        'startingRunCount': 123,
        'runningRunCount': 123,
        'stoppingRunCount': 123,
        'completedRunCount': 123,
        'deletedRunCount': 123,
        'failedRunCount': 123,
        'cancelledRunCount': 123
    },
    'creationTime': datetime(2015, 1, 1),
    'submittedTime': datetime(2015, 1, 1),
    'processedTime': datetime(2015, 1, 1),
    'failedTime': datetime(2015, 1, 1),
    'failureReason': 'string'
}

Response Structure

  • (dict) --

    • id (string) --

      The identifier portion of the run batch ARN.

    • arn (string) --

      The unique ARN of the run batch.

    • uuid (string) --

      The universally unique identifier (UUID) for the run batch.

    • name (string) --

      The optional user-friendly name of the batch.

    • status (string) --

      The current status of the run batch. Possible values: CREATING (initial setup), PENDING (ready to submit runs), SUBMITTING (submitting runs), INPROGRESS (runs executing), STOPPING (cancellation in progress), PROCESSED (all runs completed), CANCELLED (batch cancelled), FAILED (batch failed), RUNS_DELETING (deleting runs), RUNS_DELETED (runs deleted).

    • tags (dict) --

      AWS tags associated with the run batch.

      • (string) --

        • (string) --

    • totalRuns (integer) --

      The total number of runs in the batch.

    • defaultRunSetting (dict) --

      The shared configuration applied to all runs in the batch. See DefaultRunSetting.

      • workflowId (string) --

        The identifier of the workflow to run.

      • workflowType (string) --

        The type of the originating workflow. Batch runs are not supported with READY2RUN workflows.

      • roleArn (string) --

        The IAM role ARN that grants HealthOmics permissions to access required AWS resources such as Amazon S3 and CloudWatch. The role must have the same permissions required for individual StartRun calls.

      • name (string) --

        An optional user-friendly name applied to each workflow run. Can be overridden per run.

      • cacheId (string) --

        The identifier of the run cache to associate with the runs.

      • cacheBehavior (string) --

        The cache behavior for the runs. Requires cacheId to be set.

      • runGroupId (string) --

        The ID of the run group to contain all workflow runs in the batch.

      • priority (integer) --

        An integer priority for the workflow runs. Higher values correspond to higher priority. A value of 0 corresponds to the lowest priority. Can be overridden per run.

      • parameters (:ref:`document<document>`) --

        Workflow parameter names and values shared across all runs. Merged with per-run parameters; run-specific values take precedence when keys overlap. Can be overridden per run.

      • storageCapacity (integer) --

        The filesystem size in gibibytes (GiB) provisioned for each workflow run and shared by all tasks in that run. Defaults to 1200 GiB if not specified.

      • outputUri (string) --

        The destination S3 URI for workflow outputs. Must begin with s3://. The roleArn must grant write permissions to this bucket. Can be overridden per run.

      • logLevel (string) --

        The verbosity level for CloudWatch Logs emitted during each run.

      • runTags (dict) --

        AWS tags to associate with each workflow run. Merged with per-run runTags; run-specific values take precedence when keys overlap.

        • (string) --

          • (string) --

      • retentionMode (string) --

        The retention behavior for runs after completion.

      • storageType (string) --

        The storage type for the workflow runs.

      • workflowOwnerId (string) --

        The AWS account ID of the workflow owner, used for cross-account workflow sharing.

      • outputBucketOwnerId (string) --

        The expected AWS account ID of the owner of the output S3 bucket. Can be overridden per run.

      • workflowVersionName (string) --

        The version name of the specified workflow.

      • networkingMode (string) --

        Optional configuration for run networking behavior. If not specified, this will default to RESTRICTED.

      • configurationName (string) --

        Optional configuration name to use for the workflow run.

    • submissionSummary (dict) --

      A summary of run submission outcomes. See SubmissionSummary.

      • successfulStartSubmissionCount (integer) --

        The number of successful start submissions.

      • failedStartSubmissionCount (integer) --

        The number of failed start submissions.

      • pendingStartSubmissionCount (integer) --

        The number of pending start submissions.

      • successfulCancelSubmissionCount (integer) --

        The number of successful cancel submissions.

      • failedCancelSubmissionCount (integer) --

        The number of failed cancel submissions.

      • successfulDeleteSubmissionCount (integer) --

        The number of successful delete submissions.

      • failedDeleteSubmissionCount (integer) --

        The number of failed delete submissions.

    • runSummary (dict) --

      A summary of run execution states. Run execution counts are eventually consistent and may lag behind actual run states. Final counts are accurate once the batch reaches PROCESSED status. See RunSummary.

      • pendingRunCount (integer) --

        The number of pending runs.

      • startingRunCount (integer) --

        The number of starting runs.

      • runningRunCount (integer) --

        The number of running runs.

      • stoppingRunCount (integer) --

        The number of stopping runs.

      • completedRunCount (integer) --

        The number of completed runs.

      • deletedRunCount (integer) --

        The number of deleted runs.

      • failedRunCount (integer) --

        The number of failed runs.

      • cancelledRunCount (integer) --

        The number of cancelled runs.

    • creationTime (datetime) --

      The timestamp when the batch was created.

    • submittedTime (datetime) --

      The timestamp when all run submissions completed.

    • processedTime (datetime) --

      The timestamp when all run executions completed.

    • failedTime (datetime) --

      The timestamp when the batch transitioned to a FAILED status.

    • failureReason (string) --

      A description of the batch failure. Present only when status is FAILED.

ListBatch (updated) Link ¶
Changes (request, response)
Request 
{'status': {'CREATING'}}
Response 
{'items': {'status': {'CREATING'}}}

Returns a list of run batches in your account, with optional filtering by status, name, or run group. Results are paginated. Only one filter per call is supported.

See also: AWS API Documentation

Request Syntax

client.list_batch(
    maxItems=123,
    startingToken='string',
    status='CREATING'|'PENDING'|'SUBMITTING'|'INPROGRESS'|'STOPPING'|'CANCELLED'|'FAILED'|'PROCESSED'|'RUNS_DELETING'|'RUNS_DELETED',
    name='string',
    runGroupId='string'
)
type maxItems:

integer

param maxItems:

The maximum number of batches to return. If not specified, defaults to 100.

type startingToken:

string

param startingToken:

A pagination token returned from a prior ListBatch call.

type status:

string

param status:

Filter batches by status.

type name:

string

param name:

Filter batches by name.

type runGroupId:

string

param runGroupId:

Filter batches by run group ID.

rtype:

dict

returns:

Response Syntax

{
    'items': [
        {
            'id': 'string',
            'name': 'string',
            'status': 'CREATING'|'PENDING'|'SUBMITTING'|'INPROGRESS'|'STOPPING'|'CANCELLED'|'FAILED'|'PROCESSED'|'RUNS_DELETING'|'RUNS_DELETED',
            'createdAt': datetime(2015, 1, 1),
            'totalRuns': 123,
            'workflowId': 'string'
        },
    ],
    'nextToken': 'string'
}

Response Structure

  • (dict) --

    • items (list) --

      A list of batch summary objects. See BatchListItem.

      • (dict) --

        A summary of a batch returned by ListBatch.

        • id (string) --

          The batch identifier.

        • name (string) --

          The batch name.

        • status (string) --

          The current batch status.

        • createdAt (datetime) --

          The timestamp when the batch was created.

        • totalRuns (integer) --

          The total number of runs in the batch.

        • workflowId (string) --

          The identifier of the workflow used for the batch.

    • nextToken (string) --

      A pagination token to retrieve the next page of results. Absent when no further results are available.

StartRunBatch (updated) Link ¶
Changes (request, response)
Request 
{'defaultRunSetting': {'configurationName': 'string',
                       'networkingMode': 'RESTRICTED | VPC'}}
Response 
{'status': {'CREATING'}}

Starts a batch of workflow runs. You can group up to 100,000 runs into a single batch that share a common configuration defined in defaultRunSetting. Per-run overrides can be provided either inline via inlineSettings (up to 100 runs) or via a JSON file stored in Amazon S3 via s3UriSettings (up to 100,000 runs).

StartRunBatch validates common fields synchronously and returns immediately with a batch ID and status CREATING. The batch transitions to PENDING once initial setup completes. Runs are then submitted gradually and asynchronously at a rate governed by your StartRun throughput quota.

See also: AWS API Documentation

Request Syntax

client.start_run_batch(
    batchName='string',
    requestId='string',
    tags={
        'string': 'string'
    },
    defaultRunSetting={
        'workflowId': 'string',
        'workflowType': 'PRIVATE'|'READY2RUN',
        'roleArn': 'string',
        'name': 'string',
        'cacheId': 'string',
        'cacheBehavior': 'CACHE_ON_FAILURE'|'CACHE_ALWAYS',
        'runGroupId': 'string',
        'priority': 123,
        'parameters': {...}|[...]|123|123.4|'string'|True|None,
        'storageCapacity': 123,
        'outputUri': 'string',
        'logLevel': 'OFF'|'FATAL'|'ERROR'|'ALL',
        'runTags': {
            'string': 'string'
        },
        'retentionMode': 'RETAIN'|'REMOVE',
        'storageType': 'STATIC'|'DYNAMIC',
        'workflowOwnerId': 'string',
        'outputBucketOwnerId': 'string',
        'workflowVersionName': 'string',
        'networkingMode': 'RESTRICTED'|'VPC',
        'configurationName': 'string'
    },
    batchRunSettings={
        'inlineSettings': [
            {
                'runSettingId': 'string',
                'name': 'string',
                'outputUri': 'string',
                'priority': 123,
                'parameters': {...}|[...]|123|123.4|'string'|True|None,
                'outputBucketOwnerId': 'string',
                'runTags': {
                    'string': 'string'
                }
            },
        ],
        's3UriSettings': 'string'
    }
)
type batchName:

string

param batchName:

An optional user-friendly name for the run batch.

type requestId:

string

param requestId:

[REQUIRED]

A client token used to deduplicate retry requests and prevent duplicate batches from being created.

This field is autopopulated if not provided.

type tags:

dict

param tags:

AWS tags to associate with the batch resource. These tags are not inherited by individual runs. To tag individual runs, use defaultRunSetting.runTags.

  • (string) --

    • (string) --

type defaultRunSetting:

dict

param defaultRunSetting:

[REQUIRED]

Shared configuration applied to all runs in the batch. See DefaultRunSetting.

  • workflowId (string) -- [REQUIRED]

    The identifier of the workflow to run.

  • workflowType (string) --

    The type of the originating workflow. Batch runs are not supported with READY2RUN workflows.

  • roleArn (string) -- [REQUIRED]

    The IAM role ARN that grants HealthOmics permissions to access required AWS resources such as Amazon S3 and CloudWatch. The role must have the same permissions required for individual StartRun calls.

  • name (string) --

    An optional user-friendly name applied to each workflow run. Can be overridden per run.

  • cacheId (string) --

    The identifier of the run cache to associate with the runs.

  • cacheBehavior (string) --

    The cache behavior for the runs. Requires cacheId to be set.

  • runGroupId (string) --

    The ID of the run group to contain all workflow runs in the batch.

  • priority (integer) --

    An integer priority for the workflow runs. Higher values correspond to higher priority. A value of 0 corresponds to the lowest priority. Can be overridden per run.

  • parameters (:ref:`document<document>`) --

    Workflow parameter names and values shared across all runs. Merged with per-run parameters; run-specific values take precedence when keys overlap. Can be overridden per run.

  • storageCapacity (integer) --

    The filesystem size in gibibytes (GiB) provisioned for each workflow run and shared by all tasks in that run. Defaults to 1200 GiB if not specified.

  • outputUri (string) --

    The destination S3 URI for workflow outputs. Must begin with s3://. The roleArn must grant write permissions to this bucket. Can be overridden per run.

  • logLevel (string) --

    The verbosity level for CloudWatch Logs emitted during each run.

  • runTags (dict) --

    AWS tags to associate with each workflow run. Merged with per-run runTags; run-specific values take precedence when keys overlap.

    • (string) --

      • (string) --

  • retentionMode (string) --

    The retention behavior for runs after completion.

  • storageType (string) --

    The storage type for the workflow runs.

  • workflowOwnerId (string) --

    The AWS account ID of the workflow owner, used for cross-account workflow sharing.

  • outputBucketOwnerId (string) --

    The expected AWS account ID of the owner of the output S3 bucket. Can be overridden per run.

  • workflowVersionName (string) --

    The version name of the specified workflow.

  • networkingMode (string) --

    Optional configuration for run networking behavior. If not specified, this will default to RESTRICTED.

  • configurationName (string) --

    Optional configuration name to use for the workflow run.

type batchRunSettings:

dict

param batchRunSettings:

[REQUIRED]

The individual run configurations. Specify exactly one of inlineSettings or s3UriSettings. See BatchRunSettings.

  • inlineSettings (list) --

    A list of per-run configurations provided inline in the request. Each entry must include a unique runSettingId. Supports up to 100 entries. For batches with more than 100 runs, use s3UriSettings.

    • (dict) --

      A per-run configuration that overrides or merges with fields from DefaultRunSetting for a specific run.

      • runSettingId (string) -- [REQUIRED]

        A customer-provided unique identifier for this run configuration within the batch. After submission, use ListRunsInBatch to map each runSettingId to the HealthOmics-generated runId.

      • name (string) --

        An optional user-friendly name for this run.

      • outputUri (string) --

        Override the destination S3 URI for this run's outputs.

      • priority (integer) --

        Override the priority for this run.

      • parameters (:ref:`document<document>`) --

        Per-run workflow parameters. Merged with defaultRunSetting.parameters; values in this object take precedence when keys overlap.

      • outputBucketOwnerId (string) --

        The expected AWS account ID of the owner of the output S3 bucket for this run.

      • runTags (dict) --

        Per-run AWS tags. Merged with defaultRunSetting.runTags; values in this object take precedence when keys overlap.

        • (string) --

          • (string) --

  • s3UriSettings (string) --

    An Amazon S3 URI pointing to a JSON file containing per-run configurations. The file must be a JSON array in the same format as inlineSettings. Supports up to 100,000 run configurations. The maximum file size is 6 GB.

    The IAM service role in roleArn must have read access to this S3 object. HealthOmics validates access to the file during the synchronous API call and records the file's ETag. If the file is modified after submission, the batch fails.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'arn': 'string',
    'status': 'CREATING'|'PENDING'|'SUBMITTING'|'INPROGRESS'|'STOPPING'|'CANCELLED'|'FAILED'|'PROCESSED'|'RUNS_DELETING'|'RUNS_DELETED',
    'uuid': 'string',
    'tags': {
        'string': 'string'
    }
}

Response Structure

  • (dict) --

    • id (string) --

      The identifier portion of the run batch ARN.

    • arn (string) --

      The unique ARN of the run batch.

    • status (string) --

      The initial status of the run batch. Returns CREATING while the batch is being initialized.

    • uuid (string) --

      The universally unique identifier (UUID) for the run batch.

    • tags (dict) --

      AWS tags associated with the run batch.

      • (string) --

        • (string) --