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) --