Omics / Client / get_workflow

get_workflow¶

Omics.Client.get_workflow(**kwargs)¶

Gets all information about a workflow using its ID.

If a workflow is shared with you, you cannot export the workflow.

For more information about your workflow status, see Verify the workflow status in the Amazon Web Services HealthOmics User Guide.

Request Syntax

response = client.get_workflow(
    id='string',
    type='PRIVATE'|'READY2RUN',
    export=[
        'DEFINITION'|'README',
    ],
    workflowOwnerId='string'
)

Parameters:

id (string) –
[REQUIRED]

The workflow’s ID.
type (string) – The workflow’s type.
export (list) –
The export format for the workflow.
- (string) –
workflowOwnerId (string) – The ID of the workflow owner.

Return type:

dict

Returns:

Response Syntax

{
    'arn': 'string',
    'id': 'string',
    'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
    'type': 'PRIVATE'|'READY2RUN',
    'name': 'string',
    'description': 'string',
    'engine': 'WDL'|'NEXTFLOW'|'CWL'|'WDL_LENIENT',
    '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',
    'storageType': 'STATIC'|'DYNAMIC',
    'uuid': 'string',
    'containerRegistryMap': {
        'registryMappings': [
            {
                'upstreamRegistryUrl': 'string',
                'ecrRepositoryPrefix': 'string',
                'upstreamRepositoryPrefix': 'string',
                'ecrAccountId': 'string',
                'credentialArn': 'string'
            },
        ],
        'imageMappings': [
            {
                'sourceImage': 'string',
                'destinationImage': 'string'
            },
        ]
    },
    'readme': 'string',
    'definitionRepositoryDetails': {
        'connectionArn': 'string',
        'fullRepositoryId': 'string',
        'sourceReference': {
            'type': 'BRANCH'|'TAG'|'COMMIT',
            'value': 'string'
        },
        'providerType': 'string',
        'providerEndpoint': 'string'
    },
    'readmePath': 'string',
    'profiles': [
        'string',
    ],
    'profileParameterTemplates': {
        'string': {
            'string': {
                'description': 'string',
                'optional': True|False
            }
        }
    }
}

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 default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.
- 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 the workflow.
  - (string) –
    - (string) –
- accelerators (string) –
  
  The computational accelerator specified to run the workflow.
- storageType (string) –
  
  The default storage type for runs using this workflow.
- uuid (string) –
  
  The universally unique identifier (UUID) value for this workflow.
- containerRegistryMap (dict) –
  
  The registry map that this workflow is using.
  - registryMappings (list) –
    
    The mappings between upstream container registries and repository prefixes in your Amazon Elastic Container Registry (Amazon ECR) private registry. The list can include both pull through cache mappings and mappings for registries that Amazon Web Services HealthOmics copies images from.
    - (dict) –
      
      Maps an upstream container registry to a repository prefix in your Amazon Elastic Container Registry (Amazon ECR) private registry. For registries that Amazon ECR pull through cache supports, you create a pull through cache rule that synchronizes the upstream repositories with your private repositories. You can also use some registries that pull through cache doesn’t support. For these registries, specify credentialArn, and Amazon Web Services HealthOmics copies each image into a private Amazon ECR repository the first time a task needs it.
      - upstreamRegistryUrl (string) –
        
        The URI of the upstream registry.
      - ecrRepositoryPrefix (string) –
        
        The repository prefix to use in the ECR private repository.
      - upstreamRepositoryPrefix (string) –
        
        The repository prefix of the corresponding repository in the upstream registry.
      - ecrAccountId (string) –
        
        Account ID of the account that owns the upstream container image.
      - credentialArn (string) –
        
        The Amazon Resource Name (ARN) of the Amazon Web Services Secrets Manager secret that holds the credentials for the upstream registry. You must specify this value when Amazon Elastic Container Registry (Amazon ECR) doesn’t support pull through cache for the upstream registry. HealthOmics supports only some of these registries. The workflow role must have permission to call the secretsmanager:GetSecretValue operation on the secret. For more information about the supported registries, see Container images in the Amazon Web Services HealthOmics User Guide.
  - imageMappings (list) –
    
    Image mappings specify path mappings between the ECR private repository and their corresponding external repositories.
    - (dict) –
      
      Specifies image mappings that workflow tasks can use. For example, you can replace all the task references of a public image to use an equivalent image in your private ECR repository. You can use image mappings with upstream registries that don’t support pull through cache. You need to manually synchronize the upstream registry with your private repository.
      - sourceImage (string) –
        
        Specifies the URI of the source image in the upstream registry.
      - destinationImage (string) –
        
        Specifies the URI of the corresponding image in the private ECR registry.
- readme (string) –
  
  The README content for the workflow, providing documentation and usage information.
- definitionRepositoryDetails (dict) –
  
  Details about the source code repository that hosts the workflow definition files.
  - connectionArn (string) –
    
    The Amazon Resource Name (ARN) of the connection to the source code repository.
  - fullRepositoryId (string) –
    
    The full repository identifier, including the repository owner and name. For example, ‘repository-owner/repository-name’.
  - sourceReference (dict) –
    
    The source reference for the repository, such as a branch name, tag, or commit ID.
    - type (string) –
      
      The type of source reference, such as branch, tag, or commit.
    - value (string) –
      
      The value of the source reference, such as the branch name, tag name, or commit ID.
  - providerType (string) –
    
    The provider type of the source code repository, such as Bitbucket, GitHub, GitHubEnterpriseServer, GitLab, and GitLabSelfManaged.
  - providerEndpoint (string) –
    
    The endpoint URL of the source code repository provider.
- readmePath (string) –
  
  The path to the workflow README markdown file within the repository. This file provides documentation and usage information for the workflow. If not specified, the README.md file from the root directory of the repository will be used.
- profiles (list) –
  
  The list of Nextflow profiles that are available for this workflow. Profiles allow you to select predefined configuration settings at runtime.
  - (string) –
- profileParameterTemplates (dict) –
  
  A mapping of profile names to their parameter templates. Each profile defines its own set of parameters that you can use when starting a run with that profile.
  - (string) –
    - (dict) –
      - (string) –
        
        (dict) –
        
        A workflow parameter.
        
        description (string) –
        
        The parameter’s description.
        
        optional (boolean) –
        
        Whether the parameter is optional.

get_workflow¶

Request Syntax

Response Syntax

Response Structure

Exceptions