AWS API Changes

2023/02/28 - Amazon Omics - 9 updated api methods

Changes Minor model changes to accomodate batch imports feature

CreateWorkflow (updated)

Link ¶
Changes (response)

{'status': {'INACTIVE'}}

Creates a workflow.

See also: AWS API Documentation

Request Syntax

client.create_workflow(
    definitionUri='string',
    definitionZip=b'bytes',
    description='string',
    engine='WDL'|'NEXTFLOW',
    main='string',
    name='string',
    parameterTemplate={
        'string': {
            'description': 'string',
            'optional': True|False
        }
    },
    requestId='string',
    storageCapacity=123,
    tags={
        'string': 'string'
    }
)

type definitionUri:

string

param definitionUri:

The URI of a definition for the workflow.

type definitionZip:

bytes

param definitionZip:

A ZIP archive for the workflow.

type description:

string

param description:

A description for the workflow.

type engine:

string

param engine:

An engine for the workflow.

type main:

string

param main:

The path of the main definition file for the workflow.

type name:

string

param name:

A name for the workflow.

type parameterTemplate:

dict

param parameterTemplate:

A parameter template for the workflow.

(string) --
- (dict) --
  
  A workflow parameter.
  - description (string) --
    
    The parameter's description.
  - optional (boolean) --
    
    Whether the parameter is optional.

type requestId:

string

param requestId:

[REQUIRED]

To ensure that requests don't run multiple times, specify a unique ID for each request.

This field is autopopulated if not provided.

type storageCapacity:

integer

param storageCapacity:

A storage capacity for the workflow in gigabytes.

type tags:

dict

param tags:

Tags for the workflow.

(string) --
- (string) --

rtype:

dict

returns:

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) --

GetAnnotationImportJob (updated)

Link ¶
Changes (response)

{'items': {'jobStatus': {'COMPLETED_WITH_FAILURES'}},
 'status': {'COMPLETED_WITH_FAILURES'}}

Gets information about an annotation import job.

See also: AWS API Documentation

Request Syntax

client.get_annotation_import_job(
    jobId='string'
)

type jobId:

string

param jobId:

[REQUIRED]

The job's ID.

rtype:

dict

returns:

Response Syntax

{
    'completionTime': datetime(2015, 1, 1),
    'creationTime': datetime(2015, 1, 1),
    'destinationName': 'string',
    'formatOptions': {
        'tsvOptions': {
            'readOptions': {
                'comment': 'string',
                'encoding': 'string',
                'escape': 'string',
                'escapeQuotes': True|False,
                'header': True|False,
                'lineSep': 'string',
                'quote': 'string',
                'quoteAll': True|False,
                'sep': 'string'
            }
        },
        'vcfOptions': {
            'ignoreFilterField': True|False,
            'ignoreQualField': True|False
        }
    },
    'id': 'string',
    'items': [
        {
            'jobStatus': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
            'source': 'string'
        },
    ],
    'roleArn': 'string',
    'runLeftNormalization': True|False,
    'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
    'statusMessage': 'string',
    'updateTime': datetime(2015, 1, 1)
}

Response Structure

(dict) --
- completionTime (datetime) --
  
  When the job completed.
- creationTime (datetime) --
  
  When the job was created.
- destinationName (string) --
  
  The job's destination annotation store.
- formatOptions (dict) --
  
  Formatting options for a file.
  Note
  
  This is a Tagged Union structure. Only one of the following top level keys will be set: tsvOptions, vcfOptions. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
```
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
```
  - tsvOptions (dict) --
    
    Options for a TSV file.
    - readOptions (dict) --
      
      The file's read options.
      - comment (string) --
        
        The file's comment character.
      - encoding (string) --
        
        The file's encoding.
      - escape (string) --
        
        A character for escaping quotes in the file.
      - escapeQuotes (boolean) --
        
        Whether quotes need to be escaped in the file.
      - header (boolean) --
        
        Whether the file has a header row.
      - lineSep (string) --
        
        A line separator for the file.
      - quote (string) --
        
        The file's quote character.
      - quoteAll (boolean) --
        
        Whether all values need to be quoted, or just those that contain quotes.
      - sep (string) --
        
        The file's field separator.
  - vcfOptions (dict) --
    
    Options for a VCF file.
    - ignoreFilterField (boolean) --
      
      The file's ignore filter field setting.
    - ignoreQualField (boolean) --
      
      The file's ignore qual field setting.
- id (string) --
  
  The job's ID.
- items (list) --
  
  The job's imported items.
  - (dict) --
    
    Details about an imported annotation item.
    - jobStatus (string) --
      
      The item's job status.
    - source (string) --
      
      The source file's location in Amazon S3.
- roleArn (string) --
  
  The job's service role ARN.
- runLeftNormalization (boolean) --
  
  The job's left normalization setting.
- status (string) --
  
  The job's status.
- statusMessage (string) --
  
  The job's status message.
- updateTime (datetime) --
  
  When the job was updated.

GetRun (updated)

Link ¶
Changes (response)

{'workflowType': {'SERVICE'}}

Gets information about a workflow run.

See also: AWS API Documentation

Request Syntax

client.get_run(
    export=[
        'DEFINITION',
    ],
    id='string'
)

type export:

list

param export:

The run's export format.

(string) --

type id:

string

param id:

[REQUIRED]

The run's ID.

rtype:

dict

returns:

Response Syntax

{
    'arn': 'string',
    'creationTime': datetime(2015, 1, 1),
    'definition': 'string',
    'digest': 'string',
    'id': 'string',
    'logLevel': 'OFF'|'FATAL'|'ERROR'|'ALL',
    'name': 'string',
    'outputUri': 'string',
    'parameters': {...}|[...]|123|123.4|'string'|True|None,
    'priority': 123,
    'resourceDigests': {
        'string': 'string'
    },
    'roleArn': 'string',
    'runGroupId': 'string',
    'runId': 'string',
    'startTime': datetime(2015, 1, 1),
    'startedBy': 'string',
    'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED',
    'statusMessage': 'string',
    'stopTime': datetime(2015, 1, 1),
    'storageCapacity': 123,
    'tags': {
        'string': 'string'
    },
    'workflowId': 'string',
    'workflowType': 'PRIVATE'|'SERVICE'
}

Response Structure

(dict) --
- arn (string) --
  
  The run's ARN.
- creationTime (datetime) --
  
  When the run was created.
- definition (string) --
  
  The run's definition.
- digest (string) --
  
  The run's digest.
- id (string) --
  
  The run's ID.
- logLevel (string) --
  
  The run's log level.
- name (string) --
  
  The run's name.
- outputUri (string) --
  
  The run's output URI.
- parameters (:ref:`document<document>`) --
  
  The run's parameters.
- priority (integer) --
  
  The run's priority.
- resourceDigests (dict) --
  
  The run's resource digests.
  - (string) --
    - (string) --
- roleArn (string) --
  
  The run's service role ARN.
- runGroupId (string) --
  
  The run's group ID.
- runId (string) --
  
  The run's ID.
- startTime (datetime) --
  
  When the run started.
- startedBy (string) --
  
  Who started the run.
- status (string) --
  
  The run's status.
- statusMessage (string) --
  
  The run's status message.
- stopTime (datetime) --
  
  The run's stop time.
- storageCapacity (integer) --
  
  The run's storage capacity in gigabytes.
- tags (dict) --
  
  The run's tags.
  - (string) --
    - (string) --
- workflowId (string) --
  
  The run's workflow ID.
- workflowType (string) --
  
  The run's workflow type.

GetVariantImportJob (updated)

Link ¶
Changes (response)

{'items': {'jobStatus': {'COMPLETED_WITH_FAILURES'}, 'statusMessage': 'string'},
 'status': {'COMPLETED_WITH_FAILURES'}}

Gets information about a variant import job.

See also: AWS API Documentation

Request Syntax

client.get_variant_import_job(
    jobId='string'
)

type jobId:

string

param jobId:

[REQUIRED]

The job's ID.

rtype:

dict

returns:

Response Syntax

{
    'completionTime': datetime(2015, 1, 1),
    'creationTime': datetime(2015, 1, 1),
    'destinationName': 'string',
    'id': 'string',
    'items': [
        {
            'jobStatus': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
            'source': 'string',
            'statusMessage': 'string'
        },
    ],
    'roleArn': 'string',
    'runLeftNormalization': True|False,
    'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
    'statusMessage': 'string',
    'updateTime': datetime(2015, 1, 1)
}

Response Structure

(dict) --
- completionTime (datetime) --
  
  When the job completed.
- creationTime (datetime) --
  
  When the job was created.
- destinationName (string) --
  
  The job's destination variant store.
- id (string) --
  
  The job's ID.
- items (list) --
  
  The job's items.
  - (dict) --
    
    Details about an imported variant item.
    - jobStatus (string) --
      
      The item's job status.
    - source (string) --
      
      The source file's location in Amazon S3.
    - statusMessage (string) --
      
      A message that provides additional context about a job
- roleArn (string) --
  
  The job's service role ARN.
- runLeftNormalization (boolean) --
  
  The job's left normalization setting.
- status (string) --
  
  The job's status.
- statusMessage (string) --
  
  The job's status message.
- updateTime (datetime) --
  
  When the job was updated.

GetWorkflow (updated)

Link ¶
Changes (request, response)
Request

{'type': {'SERVICE'}}

Response

{'status': {'INACTIVE'}, 'type': {'SERVICE'}}

Gets information about a workflow.

See also: AWS API Documentation

Request Syntax

client.get_workflow(
    export=[
        'DEFINITION',
    ],
    id='string',
    type='PRIVATE'|'SERVICE'
)

type export:

list

param export:

The export format for the workflow.

(string) --

type id:

string

param id:

[REQUIRED]

The workflow's ID.

type type:

string

param type:

The workflow's type.

rtype:

dict

returns:

Response Syntax

{
    'arn': 'string',
    'creationTime': datetime(2015, 1, 1),
    'definition': 'string',
    'description': 'string',
    'digest': 'string',
    'engine': 'WDL'|'NEXTFLOW',
    'id': 'string',
    'main': 'string',
    'name': 'string',
    'parameterTemplate': {
        'string': {
            'description': 'string',
            'optional': True|False
        }
    },
    'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
    'statusMessage': 'string',
    'storageCapacity': 123,
    'tags': {
        'string': 'string'
    },
    'type': 'PRIVATE'|'SERVICE'
}

Response Structure

(dict) --
- arn (string) --
  
  The workflow's ARN.
- creationTime (datetime) --
  
  When the workflow was created.
- definition (string) --
  
  The workflow's definition.
- description (string) --
  
  The workflow's description.
- digest (string) --
  
  The workflow's digest.
- engine (string) --
  
  The workflow's engine.
- id (string) --
  
  The workflow's ID.
- main (string) --
  
  The path of the main definition file for the workflow.
- name (string) --
  
  The workflow's name.
- 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.
- status (string) --
  
  The workflow's status.
- statusMessage (string) --
  
  The workflow's status message.
- storageCapacity (integer) --
  
  The workflow's storage capacity in gigabytes.
- tags (dict) --
  
  The workflow's tags.
  - (string) --
    - (string) --
- type (string) --
  
  The workflow's type.

ListAnnotationImportJobs (updated)

Link ¶
Changes (request, response)
Request

{'filter': {'status': {'COMPLETED_WITH_FAILURES'}}}

Response

{'annotationImportJobs': {'status': {'COMPLETED_WITH_FAILURES'}}}

Retrieves a list of annotation import jobs.

See also: AWS API Documentation

Request Syntax

client.list_annotation_import_jobs(
    filter={
        'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
        'storeName': 'string'
    },
    ids=[
        'string',
    ],
    maxResults=123,
    nextToken='string'
)

type filter:

dict

param filter:

A filter to apply to the list.

status (string) --

A status to filter on.
storeName (string) --

A store name to filter on.

type ids:

list

param ids:

IDs of annotation import jobs to retrieve.

(string) --

type maxResults:

integer

param maxResults:

The maximum number of jobs 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.

rtype:

dict

returns:

Response Syntax

{
    'annotationImportJobs': [
        {
            'completionTime': datetime(2015, 1, 1),
            'creationTime': datetime(2015, 1, 1),
            'destinationName': 'string',
            'id': 'string',
            'roleArn': 'string',
            'runLeftNormalization': True|False,
            'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
            'updateTime': datetime(2015, 1, 1)
        },
    ],
    'nextToken': 'string'
}

Response Structure

(dict) --
- annotationImportJobs (list) --
  
  A list of jobs.
  - (dict) --
    
    An annotation import job.
    - completionTime (datetime) --
      
      When the job completed.
    - creationTime (datetime) --
      
      When the job was created.
    - destinationName (string) --
      
      The job's destination annotation store.
    - id (string) --
      
      The job's ID.
    - roleArn (string) --
      
      The job's service role ARN.
    - runLeftNormalization (boolean) --
      
      The job's left normalization setting.
    - status (string) --
      
      The job's status.
    - updateTime (datetime) --
      
      When the job was updated.
- nextToken (string) --
  
  A pagination token that's included if more results are available.

ListVariantImportJobs (updated)

Link ¶
Changes (request, response)
Request

{'filter': {'status': {'COMPLETED_WITH_FAILURES'}}}

Response

{'variantImportJobs': {'status': {'COMPLETED_WITH_FAILURES'}}}

Retrieves a list of variant import jobs.

See also: AWS API Documentation

Request Syntax

client.list_variant_import_jobs(
    filter={
        'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
        'storeName': 'string'
    },
    ids=[
        'string',
    ],
    maxResults=123,
    nextToken='string'
)

type filter:

dict

param filter:

A filter to apply to the list.

status (string) --

A status to filter on.
storeName (string) --

A store name to filter on.

type ids:

list

param ids:

A list of job IDs.

(string) --

type maxResults:

integer

param maxResults:

The maximum number of import jobs 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.

rtype:

dict

returns:

Response Syntax

{
    'nextToken': 'string',
    'variantImportJobs': [
        {
            'completionTime': datetime(2015, 1, 1),
            'creationTime': datetime(2015, 1, 1),
            'destinationName': 'string',
            'id': 'string',
            'roleArn': 'string',
            'runLeftNormalization': True|False,
            'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
            'updateTime': datetime(2015, 1, 1)
        },
    ]
}

Response Structure

(dict) --
- nextToken (string) --
  
  A pagination token that's included if more results are available.
- variantImportJobs (list) --
  
  A list of jobs.
  - (dict) --
    
    A variant import job.
    - completionTime (datetime) --
      
      When the job completed.
    - creationTime (datetime) --
      
      When the job was created.
    - destinationName (string) --
      
      The job's destination variant store.
    - id (string) --
      
      The job's ID.
    - roleArn (string) --
      
      The job's service role ARN.
    - runLeftNormalization (boolean) --
      
      The job's left normalization setting.
    - status (string) --
      
      The job's status.
    - updateTime (datetime) --
      
      When the job was updated.

ListWorkflows (updated)

Link ¶
Changes (request, response)
Request

{'type': {'SERVICE'}}

Response

{'items': {'status': {'INACTIVE'}, 'type': {'SERVICE'}}}

Retrieves a list of workflows.

See also: AWS API Documentation

Request Syntax

client.list_workflows(
    maxResults=123,
    name='string',
    startingToken='string',
    type='PRIVATE'|'SERVICE'
)

type maxResults:

integer

param maxResults:

The maximum number of workflows to return in one page of results.

type name:

string

param name:

The workflows' name.

type startingToken:

string

param startingToken:

Specify the pagination token from a previous request to retrieve the next page of results.

type type:

string

param type:

The workflows' type.

rtype:

dict

returns:

Response Syntax

{
    'items': [
        {
            'arn': 'string',
            'creationTime': datetime(2015, 1, 1),
            'digest': 'string',
            'id': 'string',
            'name': 'string',
            'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
            'type': 'PRIVATE'|'SERVICE'
        },
    ],
    'nextToken': 'string'
}

Response Structure

(dict) --
- items (list) --
  
  The workflows' items.
  - (dict) --
    
    A workflow.
    - arn (string) --
      
      The workflow's ARN.
    - creationTime (datetime) --
      
      When the workflow was created.
    - digest (string) --
      
      The workflow's digest.
    - id (string) --
      
      The workflow's ID.
    - name (string) --
      
      The workflow's name.
    - status (string) --
      
      The workflow's status.
    - type (string) --
      
      The workflow's type.
- nextToken (string) --
  
  A pagination token that's included if more results are available.

StartRun (updated)

Link ¶
Changes (request)

{'workflowType': {'SERVICE'}}

Starts a run.

See also: AWS API Documentation

Request Syntax

client.start_run(
    logLevel='OFF'|'FATAL'|'ERROR'|'ALL',
    name='string',
    outputUri='string',
    parameters={...}|[...]|123|123.4|'string'|True|None,
    priority=123,
    requestId='string',
    roleArn='string',
    runGroupId='string',
    runId='string',
    storageCapacity=123,
    tags={
        'string': 'string'
    },
    workflowId='string',
    workflowType='PRIVATE'|'SERVICE'
)

type logLevel:

string

param logLevel:

A log level for the run.

type name:

string

param name:

A name for the run.

type outputUri:

string

param outputUri:

An output URI for the run.

type parameters:

:ref:`document<document>`

param parameters:

Parameters for the run.

type priority:

integer

param priority:

A priority for the run.

type requestId:

string

param requestId:

[REQUIRED]

To ensure that requests don't run multiple times, specify a unique ID for each request.

This field is autopopulated if not provided.

type roleArn:

string

param roleArn:

[REQUIRED]

A service role for the run.

type runGroupId:

string

param runGroupId:

The run's group ID.

type runId:

string

param runId:

The run's ID.

type storageCapacity:

integer

param storageCapacity:

A storage capacity for the run in gigabytes.

type tags:

dict

param tags:

Tags for the run.

(string) --
- (string) --

type workflowId:

string

param workflowId:

The run's workflow ID.

type workflowType:

string

param workflowType:

The run's workflows type.

rtype:

dict

returns:

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) --