Class: Aws::Omics::Client

Inherits:
Seahorse::Client::Base show all
Includes:
ClientStubs
Defined in:
gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb

Overview

An API client for Omics. To construct a client, you need to configure a :region and :credentials.

client = Aws::Omics::Client.new(
  region: region_name,
  credentials: credentials,
  # ...
)

For details on configuring region and credentials see the developer guide.

See #initialize for a full list of supported configuration options.

Instance Attribute Summary

Attributes inherited from Seahorse::Client::Base

#config, #handlers

API Operations collapse

Instance Method Summary collapse

Methods included from ClientStubs

#api_requests, #stub_data, #stub_responses

Methods inherited from Seahorse::Client::Base

add_plugin, api, clear_plugins, define, new, #operation_names, plugins, remove_plugin, set_api, set_plugins

Methods included from Seahorse::Client::HandlerBuilder

#handle, #handle_request, #handle_response

Constructor Details

#initialize(options) ⇒ Client

Returns a new instance of Client.

Parameters:

  • options (Hash)

Options Hash (options):

  • :plugins (Array<Seahorse::Client::Plugin>) — default: []] —

    A list of plugins to apply to the client. Each plugin is either a class name or an instance of a plugin class.

  • :credentials (required, Aws::CredentialProvider) —

    Your AWS credentials used for authentication. This can be any class that includes and implements Aws::CredentialProvider, or instance of any one of the following classes:

    • Aws::Credentials - Used for configuring static, non-refreshing credentials.

    • Aws::SharedCredentials - Used for loading static credentials from a shared file, such as ~/.aws/config.

    • Aws::AssumeRoleCredentials - Used when you need to assume a role.

    • Aws::AssumeRoleWebIdentityCredentials - Used when you need to assume a role after providing credentials via the web.

    • Aws::SSOCredentials - Used for loading credentials from AWS SSO using an access token generated from aws login.

    • Aws::ProcessCredentials - Used for loading credentials from a process that outputs to stdout.

    • Aws::InstanceProfileCredentials - Used for loading credentials from an EC2 IMDS on an EC2 instance.

    • Aws::ECSCredentials - Used for loading credentials from instances running in ECS.

    • Aws::CognitoIdentityCredentials - Used for loading credentials from the Cognito Identity service.

    When :credentials are not configured directly, the following locations will be searched for credentials:

    • Aws.config[:credentials]

    • The :access_key_id, :secret_access_key, :session_token, and :account_id options.

    • ENV['AWS_ACCESS_KEY_ID'], ENV['AWS_SECRET_ACCESS_KEY'], ENV['AWS_SESSION_TOKEN'], and ENV['AWS_ACCOUNT_ID'].

    • ~/.aws/credentials

    • ~/.aws/config

    • EC2/ECS IMDS instance profile - When used by default, the timeouts are very aggressive. Construct and pass an instance of Aws::InstanceProfileCredentials or Aws::ECSCredentials to enable retries and extended timeouts. Instance profile credential fetching can be disabled by setting ENV['AWS_EC2_METADATA_DISABLED'] to true.

  • :region (required, String) —

    The AWS region to connect to. The configured :region is used to determine the service :endpoint. When not passed, a default :region is searched for in the following locations:

    • Aws.config[:region]
    • ENV['AWS_REGION']
    • ENV['AMAZON_REGION']
    • ENV['AWS_DEFAULT_REGION']
    • ~/.aws/credentials
    • ~/.aws/config
  • :access_key_id (String)
  • :account_id (String)
  • :active_endpoint_cache (Boolean) — default: false —

    When set to true, a thread polling for endpoints will be running in the background every 60 secs (default). Defaults to false.

  • :adaptive_retry_wait_to_fill (Boolean) — default: true —

    Used only in adaptive retry mode. When true, the request will sleep until there is sufficent client side capacity to retry the request. When false, the request will raise a RetryCapacityNotAvailableError and will not retry instead of sleeping.

  • :auth_scheme_preference (Array<String>) —

    A list of preferred authentication schemes to use when making a request. Supported values are: sigv4, sigv4a, httpBearerAuth, and noAuth. When set using ENV['AWS_AUTH_SCHEME_PREFERENCE'] or in shared config as auth_scheme_preference, the value should be a comma-separated list.

  • :client_side_monitoring (Boolean) — default: false —

    When true, client-side metrics will be collected for all API requests from this client.

  • :client_side_monitoring_client_id (String) — default: "" —

    Allows you to provide an identifier for this client which will be attached to all generated client side metrics. Defaults to an empty string.

  • :client_side_monitoring_host (String) — default: "127.0.0.1" —

    Allows you to specify the DNS hostname or IPv4 or IPv6 address that the client side monitoring agent is running on, where client metrics will be published via UDP.

  • :client_side_monitoring_port (Integer) — default: 31000 —

    Required for publishing client metrics. The port that the client side monitoring agent is running on, where client metrics will be published via UDP.

  • :client_side_monitoring_publisher (Aws::ClientSideMonitoring::Publisher) — default: Aws::ClientSideMonitoring::Publisher —

    Allows you to provide a custom client-side monitoring publisher class. By default, will use the Client Side Monitoring Agent Publisher.

  • :convert_params (Boolean) — default: true —

    When true, an attempt is made to coerce request parameters into the required types.

  • :correct_clock_skew (Boolean) — default: true —

    Used only in standard and adaptive retry modes. Specifies whether to apply a clock skew correction and retry requests with skewed client clocks.

  • :defaults_mode (String) — default: "legacy" —

    See DefaultsModeConfiguration for a list of the accepted modes and the configuration defaults that are included.

  • :disable_host_prefix_injection (Boolean) — default: false —

    When true, the SDK will not prepend the modeled host prefix to the endpoint.

  • :disable_request_compression (Boolean) — default: false —

    When set to 'true' the request body will not be compressed for supported operations.

  • :endpoint (String, URI::HTTPS, URI::HTTP) —

    Normally you should not configure the :endpoint option directly. This is normally constructed from the :region option. Configuring :endpoint is normally reserved for connecting to test or custom endpoints. The endpoint should be a URI formatted like:

    'http://example.com'
'https://example.com'
'http://example.com:123'
  • :endpoint_cache_max_entries (Integer) — default: 1000 —

    Used for the maximum size limit of the LRU cache storing endpoints data for endpoint discovery enabled operations. Defaults to 1000.

  • :endpoint_cache_max_threads (Integer) — default: 10 —

    Used for the maximum threads in use for polling endpoints to be cached, defaults to 10.

  • :endpoint_cache_poll_interval (Integer) — default: 60 —

    When :endpoint_discovery and :active_endpoint_cache is enabled, Use this option to config the time interval in seconds for making requests fetching endpoints information. Defaults to 60 sec.

  • :endpoint_discovery (Boolean) — default: false —

    When set to true, endpoint discovery will be enabled for operations when available.

  • :ignore_configured_endpoint_urls (Boolean) —

    Setting to true disables use of endpoint URLs provided via environment variables and the shared configuration file.

  • :log_formatter (Aws::Log::Formatter) — default: Aws::Log::Formatter.default —

    The log formatter.

  • :log_level (Symbol) — default: :info —

    The log level to send messages to the :logger at.

  • :logger (Logger) —

    The Logger instance to send log messages to. If this option is not set, logging will be disabled.

  • :max_attempts (Integer) — default: 3 —

    An integer representing the maximum number attempts that will be made for a single request, including the initial attempt. For example, setting this value to 5 will result in a request being retried up to 4 times. Used in standard and adaptive retry modes.

  • :profile (String) — default: "default" —

    Used when loading credentials from the shared credentials file at HOME/.aws/credentials. When not specified, 'default' is used.

  • :request_checksum_calculation (String) — default: "when_supported" —

    Determines when a checksum will be calculated for request payloads. Values are:

    • when_supported - (default) When set, a checksum will be calculated for all request payloads of operations modeled with the httpChecksum trait where requestChecksumRequired is true and/or a requestAlgorithmMember is modeled.
    • when_required - When set, a checksum will only be calculated for request payloads of operations modeled with the httpChecksum trait where requestChecksumRequired is true or where a requestAlgorithmMember is modeled and supplied.
  • :request_min_compression_size_bytes (Integer) — default: 10240 —

    The minimum size in bytes that triggers compression for request bodies. The value must be non-negative integer value between 0 and 10485780 bytes inclusive.

  • :response_checksum_validation (String) — default: "when_supported" —

    Determines when checksum validation will be performed on response payloads. Values are:

    • when_supported - (default) When set, checksum validation is performed on all response payloads of operations modeled with the httpChecksum trait where responseAlgorithms is modeled, except when no modeled checksum algorithms are supported.
    • when_required - When set, checksum validation is not performed on response payloads of operations unless the checksum algorithm is supported and the requestValidationModeMember member is set to ENABLED.
  • :retry_backoff (Proc) —

    A proc or lambda used for backoff. Defaults to 2**retries * retry_base_delay. This option is only used in the legacy retry mode.

  • :retry_base_delay (Float) — default: 0.3 —

    The base delay in seconds used by the default backoff function. This option is only used in the legacy retry mode.

  • :retry_jitter (Symbol) — default: :none —

    A delay randomiser function used by the default backoff function. Some predefined functions can be referenced by name - :none, :equal, :full, otherwise a Proc that takes and returns a number. This option is only used in the legacy retry mode.

    @see https://www.awsarchitectureblog.com/2015/03/backoff.html

  • :retry_limit (Integer) — default: 3 —

    The maximum number of times to retry failed requests. Only ~ 500 level server errors and certain ~ 400 level client errors are retried. Generally, these are throttling errors, data checksum errors, networking errors, timeout errors, auth errors, endpoint discovery, and errors from expired credentials. This option is only used in the legacy retry mode.

  • :retry_max_delay (Integer) — default: 0 —

    The maximum number of seconds to delay between retries (0 for no limit) used by the default backoff function. This option is only used in the legacy retry mode.

  • :retry_mode (String) — default: "legacy" —

    Specifies which retry algorithm to use. Values are:

    • legacy - The pre-existing retry behavior. This is default value if no retry mode is provided.

    • standard - A standardized set of retry rules across the AWS SDKs. This includes support for retry quotas, which limit the number of unsuccessful retries a client can make.

    • adaptive - An experimental retry mode that includes all the functionality of standard mode along with automatic client side throttling. This is a provisional mode that may change behavior in the future.

  • :sdk_ua_app_id (String) —

    A unique and opaque application ID that is appended to the User-Agent header as app/sdk_ua_app_id. It should have a maximum length of 50. This variable is sourced from environment variable AWS_SDK_UA_APP_ID or the shared config profile attribute sdk_ua_app_id.

  • :secret_access_key (String)
  • :session_token (String)
  • :sigv4a_signing_region_set (Array) —

    A list of regions that should be signed with SigV4a signing. When not passed, a default :sigv4a_signing_region_set is searched for in the following locations:

    • Aws.config[:sigv4a_signing_region_set]
    • ENV['AWS_SIGV4A_SIGNING_REGION_SET']
    • ~/.aws/config
  • :stub_responses (Boolean) — default: false —

    Causes the client to return stubbed responses. By default fake responses are generated and returned. You can specify the response data to return or errors to raise by calling ClientStubs#stub_responses. See ClientStubs for more information.

    Please note When response stubbing is enabled, no HTTP requests are made, and retries are disabled.

  • :telemetry_provider (Aws::Telemetry::TelemetryProviderBase) — default: Aws::Telemetry::NoOpTelemetryProvider —

    Allows you to provide a telemetry provider, which is used to emit telemetry data. By default, uses NoOpTelemetryProvider which will not record or emit any telemetry data. The SDK supports the following telemetry providers:

    • OpenTelemetry (OTel) - To use the OTel provider, install and require the opentelemetry-sdk gem and then, pass in an instance of a Aws::Telemetry::OTelProvider for telemetry provider.
  • :token_provider (Aws::TokenProvider) —

    Your Bearer token used for authentication. This can be any class that includes and implements Aws::TokenProvider, or instance of any one of the following classes:

    • Aws::StaticTokenProvider - Used for configuring static, non-refreshing tokens.

    • Aws::SSOTokenProvider - Used for loading tokens from AWS SSO using an access token generated from aws login.

    When :token_provider is not configured directly, the Aws::TokenProviderChain will be used to search for tokens configured for your profile in shared configuration files.

  • :use_dualstack_endpoint (Boolean) —

    When set to true, dualstack enabled endpoints (with .aws TLD) will be used if available.

  • :use_fips_endpoint (Boolean) —

    When set to true, fips compatible endpoints will be used if available. When a fips region is used, the region is normalized and this config is set to true.

  • :validate_params (Boolean) — default: true —

    When true, request parameters are validated before sending the request.

  • :endpoint_provider (Aws::Omics::EndpointProvider) —

    The endpoint provider used to resolve endpoints. Any object that responds to #resolve_endpoint(parameters) where parameters is a Struct similar to Aws::Omics::EndpointParameters.

  • :http_continue_timeout (Float) — default: 1 —

    The number of seconds to wait for a 100-continue response before sending the request body. This option has no effect unless the request has "Expect" header set to "100-continue". Defaults to nil which disables this behaviour. This value can safely be set per request on the session.

  • :http_idle_timeout (Float) — default: 5 —

    The number of seconds a connection is allowed to sit idle before it is considered stale. Stale connections are closed and removed from the pool before making a request.

  • :http_open_timeout (Float) — default: 15 —

    The default number of seconds to wait for response data. This value can safely be set per-request on the session.

  • :http_proxy (URI::HTTP, String) —

    A proxy to send requests through. Formatted like 'http://proxy.com:123'.

  • :http_read_timeout (Float) — default: 60 —

    The default number of seconds to wait for response data. This value can safely be set per-request on the session.

  • :http_wire_trace (Boolean) — default: false —

    When true, HTTP debug output will be sent to the :logger.

  • :on_chunk_received (Proc) —

    When a Proc object is provided, it will be used as callback when each chunk of the response body is received. It provides three arguments: the chunk, the number of bytes received, and the total number of bytes in the response (or nil if the server did not send a content-length).

  • :on_chunk_sent (Proc) —

    When a Proc object is provided, it will be used as callback when each chunk of the request body is sent. It provides three arguments: the chunk, the number of bytes read from the body, and the total number of bytes in the body.

  • :raise_response_errors (Boolean) — default: true —

    When true, response errors are raised.

  • :ssl_ca_bundle (String) —

    Full path to the SSL certificate authority bundle file that should be used when verifying peer certificates. If you do not pass :ssl_ca_bundle or :ssl_ca_directory the the system default will be used if available.

  • :ssl_ca_directory (String) —

    Full path of the directory that contains the unbundled SSL certificate authority files for verifying peer certificates. If you do not pass :ssl_ca_bundle or :ssl_ca_directory the the system default will be used if available.

  • :ssl_ca_store (String) —

    Sets the X509::Store to verify peer certificate.

  • :ssl_cert (OpenSSL::X509::Certificate) —

    Sets a client certificate when creating http connections.

  • :ssl_key (OpenSSL::PKey) —

    Sets a client key when creating http connections.

  • :ssl_timeout (Float) —

    Sets the SSL timeout in seconds

  • :ssl_verify_peer (Boolean) — default: true —

    When true, SSL peer certificates are verified when establishing a connection.



473
474
475
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 473

def initialize(*args)
  super
end

Instance Method Details

#abort_multipart_read_set_upload(params = {}) ⇒ Struct

Stops a multipart upload.

Examples:

Request syntax with placeholder values


resp = client.abort_multipart_read_set_upload({
  sequence_store_id: "SequenceStoreId", # required
  upload_id: "UploadId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The sequence store ID for the store involved in the multipart upload.

  • :upload_id (required, String) —

    The ID for the multipart upload.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



500
501
502
503
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 500

def abort_multipart_read_set_upload(params = {}, options = {})
  req = build_request(:abort_multipart_read_set_upload, params)
  req.send_request(options)
end

#accept_share(params = {}) ⇒ Types::AcceptShareResponse

Accept a resource share request.

Examples:

Request syntax with placeholder values


resp = client.accept_share({
  share_id: "String", # required
})

Response structure


resp.status #=> String, one of "PENDING", "ACTIVATING", "ACTIVE", "DELETING", "DELETED", "FAILED"

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :share_id (required, String) —

    The ID of the resource share.

Returns:

See Also:



528
529
530
531
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 528

def accept_share(params = {}, options = {})
  req = build_request(:accept_share, params)
  req.send_request(options)
end

#batch_delete_read_set(params = {}) ⇒ Types::BatchDeleteReadSetResponse

Deletes one or more read sets.

Examples:

Request syntax with placeholder values


resp = client.batch_delete_read_set({
  ids: ["ReadSetId"], # required
  sequence_store_id: "SequenceStoreId", # required
})

Response structure


resp.errors #=> Array
resp.errors[0].id #=> String
resp.errors[0].code #=> String
resp.errors[0].message #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :ids (required, Array<String>) —

    The read sets' IDs.

  • :sequence_store_id (required, String) —

    The read sets' sequence store ID.

Returns:

See Also:



563
564
565
566
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 563

def batch_delete_read_set(params = {}, options = {})
  req = build_request(:batch_delete_read_set, params)
  req.send_request(options)
end

#cancel_annotation_import_job(params = {}) ⇒ Struct

Cancels an annotation import job.

Examples:

Request syntax with placeholder values


resp = client.cancel_annotation_import_job({
  job_id: "ResourceId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :job_id (required, String) —

    The job's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



585
586
587
588
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 585

def cancel_annotation_import_job(params = {}, options = {})
  req = build_request(:cancel_annotation_import_job, params)
  req.send_request(options)
end

#cancel_run(params = {}) ⇒ Struct

Cancels a run using its ID and returns a response with no body if the operation is successful. To confirm that the run has been cancelled, use the ListRuns API operation to check that it is no longer listed.

Examples:

Request syntax with placeholder values


resp = client.cancel_run({
  id: "RunId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The run's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



609
610
611
612
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 609

def cancel_run(params = {}, options = {})
  req = build_request(:cancel_run, params)
  req.send_request(options)
end

#cancel_variant_import_job(params = {}) ⇒ Struct

Cancels a variant import job.

Examples:

Request syntax with placeholder values


resp = client.cancel_variant_import_job({
  job_id: "ResourceId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :job_id (required, String) —

    The job's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



631
632
633
634
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 631

def cancel_variant_import_job(params = {}, options = {})
  req = build_request(:cancel_variant_import_job, params)
  req.send_request(options)
end

#complete_multipart_read_set_upload(params = {}) ⇒ Types::CompleteMultipartReadSetUploadResponse

Concludes a multipart upload once you have uploaded all the components.

Examples:

Request syntax with placeholder values


resp = client.complete_multipart_read_set_upload({
  sequence_store_id: "SequenceStoreId", # required
  upload_id: "UploadId", # required
  parts: [ # required
    {
      part_number: 1, # required
      part_source: "SOURCE1", # required, accepts SOURCE1, SOURCE2
      checksum: "CompleteReadSetUploadPartListItemChecksumString", # required
    },
  ],
})

Response structure


resp.read_set_id #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The sequence store ID for the store involved in the multipart upload.

  • :upload_id (required, String) —

    The ID for the multipart upload.

  • :parts (required, Array<Types::CompleteReadSetUploadPartListItem>) —

    The individual uploads or parts of a multipart upload.

Returns:

See Also:



674
675
676
677
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 674

def complete_multipart_read_set_upload(params = {}, options = {})
  req = build_request(:complete_multipart_read_set_upload, params)
  req.send_request(options)
end

#create_annotation_store(params = {}) ⇒ Types::CreateAnnotationStoreResponse

Creates an annotation store.

Examples:

Request syntax with placeholder values


resp = client.create_annotation_store({
  reference: {
    reference_arn: "ReferenceArn",
  },
  name: "StoreName",
  description: "Description",
  tags: {
    "TagKey" => "TagValue",
  },
  version_name: "VersionName",
  sse_config: {
    type: "KMS", # required, accepts KMS
    key_arn: "SseConfigKeyArnString",
  },
  store_format: "GFF", # required, accepts GFF, TSV, VCF
  store_options: {
    tsv_store_options: {
      annotation_type: "GENERIC", # accepts GENERIC, CHR_POS, CHR_POS_REF_ALT, CHR_START_END_ONE_BASE, CHR_START_END_REF_ALT_ONE_BASE, CHR_START_END_ZERO_BASE, CHR_START_END_REF_ALT_ZERO_BASE
      format_to_header: {
        "CHR" => "FormatToHeaderValueString",
      },
      schema: [
        {
          "SchemaItemKeyString" => "LONG", # accepts LONG, INT, STRING, FLOAT, DOUBLE, BOOLEAN
        },
      ],
    },
  },
})

Response structure


resp.id #=> String
resp.reference.reference_arn #=> String
resp.store_format #=> String, one of "GFF", "TSV", "VCF"
resp.store_options.tsv_store_options.annotation_type #=> String, one of "GENERIC", "CHR_POS", "CHR_POS_REF_ALT", "CHR_START_END_ONE_BASE", "CHR_START_END_REF_ALT_ONE_BASE", "CHR_START_END_ZERO_BASE", "CHR_START_END_REF_ALT_ZERO_BASE"
resp.store_options.tsv_store_options.format_to_header #=> Hash
resp.store_options.tsv_store_options.format_to_header["FormatToHeaderKey"] #=> String
resp.store_options.tsv_store_options.schema #=> Array
resp.store_options.tsv_store_options.schema[0] #=> Hash
resp.store_options.tsv_store_options.schema[0]["SchemaItemKeyString"] #=> String, one of "LONG", "INT", "STRING", "FLOAT", "DOUBLE", "BOOLEAN"
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.name #=> String
resp.version_name #=> String
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :reference (Types::ReferenceItem) —

    The genome reference for the store's annotations.

  • :name (String) —

    A name for the store.

  • :description (String) —

    A description for the store.

  • :tags (Hash<String,String>) —

    Tags for the store.

  • :version_name (String) —

    The name given to an annotation store version to distinguish it from other versions.

  • :sse_config (Types::SseConfig) —

    Server-side encryption (SSE) settings for the store.

  • :store_format (required, String) —

    The annotation file format of the store.

  • :store_options (Types::StoreOptions) —

    File parsing options for the annotation store.

Returns:

See Also:



769
770
771
772
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 769

def create_annotation_store(params = {}, options = {})
  req = build_request(:create_annotation_store, params)
  req.send_request(options)
end

#create_annotation_store_version(params = {}) ⇒ Types::CreateAnnotationStoreVersionResponse

Creates a new version of an annotation store.

Examples:

Request syntax with placeholder values


resp = client.create_annotation_store_version({
  name: "StoreName", # required
  version_name: "VersionName", # required
  description: "Description",
  version_options: {
    tsv_version_options: {
      annotation_type: "GENERIC", # accepts GENERIC, CHR_POS, CHR_POS_REF_ALT, CHR_START_END_ONE_BASE, CHR_START_END_REF_ALT_ONE_BASE, CHR_START_END_ZERO_BASE, CHR_START_END_REF_ALT_ZERO_BASE
      format_to_header: {
        "CHR" => "FormatToHeaderValueString",
      },
      schema: [
        {
          "SchemaItemKeyString" => "LONG", # accepts LONG, INT, STRING, FLOAT, DOUBLE, BOOLEAN
        },
      ],
    },
  },
  tags: {
    "TagKey" => "TagValue",
  },
})

Response structure


resp.id #=> String
resp.version_name #=> String
resp.store_id #=> String
resp.version_options.tsv_version_options.annotation_type #=> String, one of "GENERIC", "CHR_POS", "CHR_POS_REF_ALT", "CHR_START_END_ONE_BASE", "CHR_START_END_REF_ALT_ONE_BASE", "CHR_START_END_ZERO_BASE", "CHR_START_END_REF_ALT_ZERO_BASE"
resp.version_options.tsv_version_options.format_to_header #=> Hash
resp.version_options.tsv_version_options.format_to_header["FormatToHeaderKey"] #=> String
resp.version_options.tsv_version_options.schema #=> Array
resp.version_options.tsv_version_options.schema[0] #=> Hash
resp.version_options.tsv_version_options.schema[0]["SchemaItemKeyString"] #=> String, one of "LONG", "INT", "STRING", "FLOAT", "DOUBLE", "BOOLEAN"
resp.name #=> String
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The name of an annotation store version from which versions are being created.

  • :version_name (required, String) —

    The name given to an annotation store version to distinguish it from other versions.

  • :description (String) —

    The description of an annotation store version.

  • :version_options (Types::VersionOptions) —

    The options for an annotation store version.

  • :tags (Hash<String,String>) —

    Any tags added to annotation store version.

Returns:

See Also:



846
847
848
849
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 846

def create_annotation_store_version(params = {}, options = {})
  req = build_request(:create_annotation_store_version, params)
  req.send_request(options)
end

#create_multipart_read_set_upload(params = {}) ⇒ Types::CreateMultipartReadSetUploadResponse

Begins a multipart read set upload.

Examples:

Request syntax with placeholder values


resp = client.create_multipart_read_set_upload({
  sequence_store_id: "SequenceStoreId", # required
  client_token: "ClientToken",
  source_file_type: "FASTQ", # required, accepts FASTQ, BAM, CRAM, UBAM
  subject_id: "SubjectId", # required
  sample_id: "SampleId", # required
  generated_from: "GeneratedFrom",
  reference_arn: "ReferenceArn",
  name: "ReadSetName", # required
  description: "ReadSetDescription",
  tags: {
    "TagKey" => "TagValue",
  },
})

Response structure


resp.sequence_store_id #=> String
resp.upload_id #=> String
resp.source_file_type #=> String, one of "FASTQ", "BAM", "CRAM", "UBAM"
resp.subject_id #=> String
resp.sample_id #=> String
resp.generated_from #=> String
resp.reference_arn #=> String
resp.name #=> String
resp.description #=> String
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The sequence store ID for the store that is the destination of the multipart uploads.

  • :client_token (String) —

    An idempotency token that can be used to avoid triggering multiple multipart uploads.

  • :source_file_type (required, String) —

    The type of file being uploaded.

  • :subject_id (required, String) —

    The source's subject ID.

  • :sample_id (required, String) —

    The source's sample ID.

  • :generated_from (String) —

    Where the source originated.

  • :reference_arn (String) —

    The ARN of the reference.

  • :name (required, String) —

    The name of the read set.

  • :description (String) —

    The description of the read set.

  • :tags (Hash<String,String>) —

    Any tags to add to the read set.

Returns:

See Also:



935
936
937
938
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 935

def create_multipart_read_set_upload(params = {}, options = {})
  req = build_request(:create_multipart_read_set_upload, params)
  req.send_request(options)
end

#create_reference_store(params = {}) ⇒ Types::CreateReferenceStoreResponse

Creates a reference store.

Examples:

Request syntax with placeholder values


resp = client.create_reference_store({
  name: "ReferenceStoreName", # required
  description: "ReferenceStoreDescription",
  sse_config: {
    type: "KMS", # required, accepts KMS
    key_arn: "SseConfigKeyArnString",
  },
  tags: {
    "TagKey" => "TagValue",
  },
  client_token: "ClientToken",
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.name #=> String
resp.description #=> String
resp.sse_config.type #=> String, one of "KMS"
resp.sse_config.key_arn #=> String
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    A name for the store.

  • :description (String) —

    A description for the store.

  • :sse_config (Types::SseConfig) —

    Server-side encryption (SSE) settings for the store.

  • :tags (Hash<String,String>) —

    Tags for the store.

  • :client_token (String) —

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

Returns:

See Also:



996
997
998
999
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 996

def create_reference_store(params = {}, options = {})
  req = build_request(:create_reference_store, params)
  req.send_request(options)
end

#create_run_cache(params = {}) ⇒ Types::CreateRunCacheResponse

Creates a run cache to store and reference task outputs from completed private runs. Specify an Amazon S3 location where Amazon Web Services HealthOmics saves the cached data. This data must be immediately accessible and not in an archived state. You can save intermediate task files to a run cache if they are declared as task outputs in the workflow definition file.

For more information, see Call caching and Creating a run cache in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.create_run_cache({
  cache_behavior: "CACHE_ON_FAILURE", # accepts CACHE_ON_FAILURE, CACHE_ALWAYS
  cache_s3_location: "S3UriForBucketOrObject", # required
  description: "UserCustomDescription",
  name: "UserCustomName",
  request_id: "RunCacheRequestId", # required
  tags: {
    "TagKey" => "TagValue",
  },
  cache_bucket_owner_id: "AwsAccountId",
})

Response structure


resp.arn #=> String
resp.id #=> String
resp.status #=> String, one of "ACTIVE", "DELETED", "FAILED"
resp.tags #=> Hash
resp.tags["TagKey"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :cache_behavior (String) —

    Default cache behavior for runs that use this cache. Supported values are:

    CACHE_ON_FAILURE: Caches task outputs from completed tasks for runs that fail. This setting is useful if you're debugging a workflow that fails after several tasks completed successfully. The subsequent run uses the cache outputs for previously-completed tasks if the task definition, inputs, and container in ECR are identical to the prior run.

    CACHE_ALWAYS: Caches task outputs from completed tasks for all runs. This setting is useful in development mode, but do not use it in a production setting.

    If you don't specify a value, the default behavior is CACHE_ON_FAILURE. When you start a run that uses this cache, you can override the default cache behavior.

    For more information, see Run cache behavior in the Amazon Web Services HealthOmics User Guide.

  • :cache_s3_location (required, String) —

    Specify the S3 location for storing the cached task outputs. This data must be immediately accessible (not in an archived state).

  • :description (String) —

    Enter a description of the run cache.

  • :name (String) —

    Enter a user-friendly name for the run cache.

  • :request_id (required, String) —

    A unique request token, to ensure idempotency. If you don't specify a token, Amazon Web Services HealthOmics automatically generates a universally unique identifier (UUID) for the request.

    A suitable default value is auto-generated. You should normally not need to pass this option.**

  • :tags (Hash<String,String>) —

    Specify one or more tags to associate with this run cache.

  • :cache_bucket_owner_id (String) —

    The Amazon Web Services account ID of the expected owner of the S3 bucket for the run cache. If not provided, your account ID is set as the owner of the bucket.

Returns:

See Also:



1101
1102
1103
1104
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1101

def create_run_cache(params = {}, options = {})
  req = build_request(:create_run_cache, params)
  req.send_request(options)
end

#create_run_group(params = {}) ⇒ Types::CreateRunGroupResponse

Creates a run group to limit the compute resources for the runs that are added to the group. Returns an ARN, ID, and tags for the run group.

Examples:

Request syntax with placeholder values


resp = client.create_run_group({
  name: "RunGroupName",
  max_cpus: 1,
  max_runs: 1,
  max_duration: 1,
  tags: {
    "TagKey" => "TagValue",
  },
  request_id: "RunGroupRequestId", # required
  max_gpus: 1,
})

Response structure


resp.arn #=> String
resp.id #=> String
resp.tags #=> Hash
resp.tags["TagKey"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (String) —

    A name for the group.

  • :max_cpus (Integer) —

    The maximum number of CPUs that can run concurrently across all active runs in the run group.

  • :max_runs (Integer) —

    The maximum number of runs that can be running at the same time.

  • :max_duration (Integer) —

    The maximum time for each run (in minutes). If a run exceeds the maximum run time, the run fails automatically.

  • :tags (Hash<String,String>) —

    Tags for the group.

  • :request_id (required, String) —

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

    A suitable default value is auto-generated. You should normally not need to pass this option.**

  • :max_gpus (Integer) —

    The maximum number of GPUs that can run concurrently across all active runs in the run group.

Returns:

See Also:



1169
1170
1171
1172
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1169

def create_run_group(params = {}, options = {})
  req = build_request(:create_run_group, params)
  req.send_request(options)
end

#create_sequence_store(params = {}) ⇒ Types::CreateSequenceStoreResponse

Creates a sequence store.

Examples:

Request syntax with placeholder values


resp = client.create_sequence_store({
  name: "SequenceStoreName", # required
  description: "SequenceStoreDescription",
  sse_config: {
    type: "KMS", # required, accepts KMS
    key_arn: "SseConfigKeyArnString",
  },
  tags: {
    "TagKey" => "TagValue",
  },
  client_token: "ClientToken",
  fallback_location: "FallbackLocation",
  e_tag_algorithm_family: "MD5up", # accepts MD5up, SHA256up, SHA512up
  propagated_set_level_tags: ["TagKey"],
  s3_access_config: {
    access_log_location: "AccessLogLocation",
  },
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.name #=> String
resp.description #=> String
resp.sse_config.type #=> String, one of "KMS"
resp.sse_config.key_arn #=> String
resp.creation_time #=> Time
resp.fallback_location #=> String
resp.e_tag_algorithm_family #=> String, one of "MD5up", "SHA256up", "SHA512up"
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETING", "FAILED"
resp.status_message #=> String
resp.propagated_set_level_tags #=> Array
resp.propagated_set_level_tags[0] #=> String
resp.s3_access.s3_uri #=> String
resp.s3_access.s3_access_point_arn #=> String
resp.s3_access.access_log_location #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    A name for the store.

  • :description (String) —

    A description for the store.

  • :sse_config (Types::SseConfig) —

    Server-side encryption (SSE) settings for the store.

  • :tags (Hash<String,String>) —

    Tags for the store.

  • :client_token (String) —

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

    A suitable default value is auto-generated. You should normally not need to pass this option.**

  • :fallback_location (String) —

    An S3 location that is used to store files that have failed a direct upload.

  • :e_tag_algorithm_family (String) —

    The ETag algorithm family to use for ingested read sets.

  • :propagated_set_level_tags (Array<String>) —

    The tags keys to propagate to the S3 objects associated with read sets in the sequence store.

  • :s3_access_config (Types::S3AccessConfig) —

    S3 access configuration parameters

Returns:

See Also:



1268
1269
1270
1271
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1268

def create_sequence_store(params = {}, options = {})
  req = build_request(:create_sequence_store, params)
  req.send_request(options)
end

#create_share(params = {}) ⇒ Types::CreateShareResponse

Creates a cross-account shared resource. The resource owner makes an offer to share the resource with the principal subscriber (an AWS user with a different account than the resource owner).

The following resources support cross-account sharing:

  • HealthOmics variant stores

  • HealthOmics annotation stores

  • Private workflows

Examples:

Request syntax with placeholder values


resp = client.create_share({
  resource_arn: "String", # required
  principal_subscriber: "String", # required
  share_name: "ShareName",
})

Response structure


resp.share_id #=> String
resp.status #=> String, one of "PENDING", "ACTIVATING", "ACTIVE", "DELETING", "DELETED", "FAILED"
resp.share_name #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :resource_arn (required, String) —

    The ARN of the resource to be shared.

  • :principal_subscriber (required, String) —

    The principal subscriber is the account being offered shared access to the resource.

  • :share_name (String) —

    A name that the owner defines for the share.

Returns:

See Also:



1319
1320
1321
1322
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1319

def create_share(params = {}, options = {})
  req = build_request(:create_share, params)
  req.send_request(options)
end

#create_variant_store(params = {}) ⇒ Types::CreateVariantStoreResponse

Creates a variant store.

Examples:

Request syntax with placeholder values


resp = client.create_variant_store({
  reference: { # required
    reference_arn: "ReferenceArn",
  },
  name: "StoreName",
  description: "Description",
  tags: {
    "TagKey" => "TagValue",
  },
  sse_config: {
    type: "KMS", # required, accepts KMS
    key_arn: "SseConfigKeyArnString",
  },
})

Response structure


resp.id #=> String
resp.reference.reference_arn #=> String
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.name #=> String
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :reference (required, Types::ReferenceItem) —

    The genome reference for the store's variants.

  • :name (String) —

    A name for the store.

  • :description (String) —

    A description for the store.

  • :tags (Hash<String,String>) —

    Tags for the store.

  • :sse_config (Types::SseConfig) —

    Server-side encryption (SSE) settings for the store.

Returns:

See Also:



1378
1379
1380
1381
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1378

def create_variant_store(params = {}, options = {})
  req = build_request(:create_variant_store, params)
  req.send_request(options)
end

#create_workflow(params = {}) ⇒ Types::CreateWorkflowResponse

Creates a private workflow. Before you create a private workflow, you must create and configure these required resources:

  • Workflow definition files: Define your workflow in one or more workflow definition files, written in WDL, Nextflow, or CWL. The workflow definition specifies the inputs and outputs for runs that use the workflow. It also includes specifications for the runs and run tasks for your workflow, including compute and memory requirements. The workflow definition file must be in .zip format.

  • (Optional) Parameter template: You can create a parameter template file that defines the run parameters, or Amazon Web Services HealthOmics can generate the parameter template for you.

  • ECR container images: Create one or more container images for the workflow. Store the images in a private ECR repository.

  • (Optional) Sentieon licenses: Request a Sentieon license if using the Sentieon software in a private workflow.

For more information, see Creating or updating a private workflow in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.create_workflow({
  name: "WorkflowName",
  description: "WorkflowDescription",
  engine: "WDL", # accepts WDL, NEXTFLOW, CWL
  definition_zip: "data",
  definition_uri: "WorkflowDefinition",
  main: "WorkflowMain",
  parameter_template: {
    "WorkflowParameterName" => {
      description: "WorkflowParameterDescription",
      optional: false,
    },
  },
  storage_capacity: 1,
  tags: {
    "TagKey" => "TagValue",
  },
  request_id: "WorkflowRequestId", # required
  accelerators: "GPU", # accepts GPU
  storage_type: "STATIC", # accepts STATIC, DYNAMIC
  readme_markdown: "ReadmeMarkdown",
  parameter_template_path: "ParameterTemplatePath",
  readme_path: "ReadmePath",
  definition_repository: {
    connection_arn: "ConnectionArn", # required
    full_repository_id: "FullRepositoryId", # required
    source_reference: {
      type: "BRANCH", # required, accepts BRANCH, TAG, COMMIT
      value: "SourceReferenceValue", # required
    },
    exclude_file_patterns: ["String"],
  },
  workflow_bucket_owner_id: "WorkflowBucketOwnerId",
  readme_uri: "S3UriForObject",
})

Response structure


resp.arn #=> String
resp.id #=> String
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETED", "FAILED", "INACTIVE"
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.uuid #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (String) —

    Name (optional but highly recommended) for the workflow to locate relevant information in the CloudWatch logs and Amazon Web Services HealthOmics console.

  • :description (String) —

    A description for the workflow.

  • :engine (String) —

    The workflow engine for the workflow. This is only required if you have workflow definition files from more than one engine in your zip file. Otherwise, the service can detect the engine automatically from your workflow definition.

  • :definition_zip (String, StringIO, File) —

    A ZIP archive containing the main workflow definition file and dependencies that it imports for the workflow. You can use a file with a ://fileb prefix instead of the Base64 string. For more information, see Workflow definition requirements in the Amazon Web Services HealthOmics User Guide.

  • :definition_uri (String) —

    The S3 URI of a definition for the workflow. The S3 bucket must be in the same region as the workflow.

  • :main (String) —

    The path of the main definition file for the workflow. This parameter is not required if the ZIP archive contains only one workflow definition file, or if the main definition file is named “main”. An example path is: workflow-definition/main-file.wdl.

  • :parameter_template (Hash<String,Types::WorkflowParameter>) —

    A parameter template for the workflow. If this field is blank, Amazon Web Services HealthOmics will automatically parse the parameter template values from your workflow definition file. To override these service generated default values, provide a parameter template. To view an example of a parameter template, see Parameter template files in the Amazon Web Services HealthOmics User Guide.

  • :storage_capacity (Integer) —

    The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version. The storageCapacity can be overwritten at run time. The storage capacity is not required for runs with a DYNAMIC storage type.

  • :tags (Hash<String,String>) —

    Tags for the workflow. You can define up to 50 tags for the workflow. For more information, see Adding a tag in the Amazon Web Services HealthOmics User Guide.

  • :request_id (required, String) —

    An idempotency token to ensure that duplicate workflows are not created when Amazon Web Services HealthOmics submits retry requests.

    A suitable default value is auto-generated. You should normally not need to pass this option.**

  • :accelerators (String) —

    The computational accelerator specified to run the workflow.

  • :storage_type (String) —

    The default storage type for runs that use this workflow. The storageType can be overridden at run time. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. STATIC storage allocates a fixed amount of storage. For more information about dynamic and static storage types, see Run storage types in the Amazon Web Services HealthOmics User Guide.

  • :readme_markdown (String) —

    The markdown content for the workflow's README file. This provides documentation and usage information for users of the workflow.

  • :parameter_template_path (String) —

    The path to the workflow parameter template JSON file within the repository. This file defines the input parameters for runs that use this workflow. If not specified, the workflow will be created without a parameter template.

  • :readme_path (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.

  • :definition_repository (Types::DefinitionRepository) —

    The repository information for the workflow definition. This allows you to source your workflow definition directly from a code repository.

  • :workflow_bucket_owner_id (String) —

    The Amazon Web Services account ID of the expected owner of the S3 bucket that contains the workflow definition. If not specified, the service skips the validation.

  • :readme_uri (String) —

    The S3 URI of the README file for the workflow. This file provides documentation and usage information for the workflow. Requirements include:

    • The S3 URI must begin with s3://USER-OWNED-BUCKET/

    • The requester must have access to the S3 bucket and object.

    • The max README content length is 500 KiB.

Returns:

See Also:



1591
1592
1593
1594
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1591

def create_workflow(params = {}, options = {})
  req = build_request(:create_workflow, params)
  req.send_request(options)
end

#create_workflow_version(params = {}) ⇒ Types::CreateWorkflowVersionResponse

Creates a new workflow version for the workflow that you specify with the workflowId parameter.

When you create a new version of a workflow, you need to specify the configuration for the new version. It doesn't inherit any configuration values from the workflow.

Provide a version name that is unique for this workflow. You cannot change the name after HealthOmics creates the version.

Don’t include any personally identifiable information (PII) in the version name. Version names appear in the workflow version ARN.

For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.create_workflow_version({
  workflow_id: "WorkflowId", # required
  version_name: "WorkflowVersionName", # required
  definition_zip: "data",
  definition_uri: "WorkflowDefinition",
  accelerators: "GPU", # accepts GPU
  description: "WorkflowVersionDescription",
  engine: "WDL", # accepts WDL, NEXTFLOW, CWL
  main: "WorkflowMain",
  parameter_template: {
    "WorkflowParameterName" => {
      description: "WorkflowParameterDescription",
      optional: false,
    },
  },
  request_id: "WorkflowRequestId", # required
  storage_type: "STATIC", # accepts STATIC, DYNAMIC
  storage_capacity: 1,
  tags: {
    "TagKey" => "TagValue",
  },
  workflow_bucket_owner_id: "WorkflowBucketOwnerId",
  readme_markdown: "ReadmeMarkdown",
  parameter_template_path: "ParameterTemplatePath",
  readme_path: "ReadmePath",
  definition_repository: {
    connection_arn: "ConnectionArn", # required
    full_repository_id: "FullRepositoryId", # required
    source_reference: {
      type: "BRANCH", # required, accepts BRANCH, TAG, COMMIT
      value: "SourceReferenceValue", # required
    },
    exclude_file_patterns: ["String"],
  },
  readme_uri: "S3UriForObject",
})

Response structure


resp.arn #=> String
resp.workflow_id #=> String
resp.version_name #=> String
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETED", "FAILED", "INACTIVE"
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.uuid #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :workflow_id (required, String) —

    The ID of the workflow where you are creating the new version.

  • :version_name (required, String) —

    A name for the workflow version. Provide a version name that is unique for this workflow. You cannot change the name after HealthOmics creates the version.

    The version name must start with a letter or number and it can include upper-case and lower-case letters, numbers, hyphens, periods and underscores. The maximum length is 64 characters. You can use a simple naming scheme, such as version1, version2, version3. You can also match your workflow versions with your own internal versioning conventions, such as 2.7.0, 2.7.1, 2.7.2.

  • :definition_zip (String, StringIO, File) —

    A zip archive containing the workflow definition for this workflow version.

  • :definition_uri (String) —

    The URI specifies the location of the workflow definition for this workflow version.

  • :accelerators (String) —

    The computational accelerator for this workflow version.

  • :description (String) —

    A description for this workflow version.

  • :engine (String) —

    The workflow engine for this workflow version.

  • :main (String) —

    The path of the main definition file for this workflow version.

  • :parameter_template (Hash<String,Types::WorkflowParameter>) —

    The parameter template defines the input parameters for runs that use this workflow version.

  • :request_id (required, String) —

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

    A suitable default value is auto-generated. You should normally not need to pass this option.**

  • :storage_type (String) —

    The default storage type for runs that use this workflow. STATIC storage allocates a fixed amount of storage. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. For more information about static and dynamic storage, see Running workflows in the Amazon Web Services HealthOmics User Guide.

  • :storage_capacity (Integer) —

    The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.

  • :tags (Hash<String,String>) —

    Optional tags to associate with this workflow version.

  • :workflow_bucket_owner_id (String) —

    Amazon Web Services Id of the owner of the S3 bucket that contains the workflow definition. You need to specify this parameter if your account is not the bucket owner.

  • :readme_markdown (String) —

    The markdown content for the workflow version's README file. This provides documentation and usage information for users of this specific workflow version.

  • :parameter_template_path (String) —

    The path to the workflow version parameter template JSON file within the repository. This file defines the input parameters for runs that use this workflow version. If not specified, the workflow version will be created without a parameter template.

  • :readme_path (String) —

    The path to the workflow version 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.

  • :definition_repository (Types::DefinitionRepository) —

    The repository information for the workflow version definition. This allows you to source your workflow version definition directly from a code repository.

  • :readme_uri (String) —

    The S3 URI of the README file for the workflow version. This file provides documentation and usage information for the workflow version. Requirements include:

    • The S3 URI must begin with s3://USER-OWNED-BUCKET/

    • The requester must have access to the S3 bucket and object.

    • The max README content length is 500 KiB.

Returns:

See Also:



1783
1784
1785
1786
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1783

def create_workflow_version(params = {}, options = {})
  req = build_request(:create_workflow_version, params)
  req.send_request(options)
end

#delete_annotation_store(params = {}) ⇒ Types::DeleteAnnotationStoreResponse

Deletes an annotation store.

Examples:

Request syntax with placeholder values


resp = client.delete_annotation_store({
  name: "String", # required
  force: false,
})

Response structure


resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The store's name.

  • :force (Boolean) —

    Whether to force deletion.

Returns:

See Also:



1815
1816
1817
1818
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1815

def delete_annotation_store(params = {}, options = {})
  req = build_request(:delete_annotation_store, params)
  req.send_request(options)
end

#delete_annotation_store_versions(params = {}) ⇒ Types::DeleteAnnotationStoreVersionsResponse

Deletes one or multiple versions of an annotation store.

Examples:

Request syntax with placeholder values


resp = client.delete_annotation_store_versions({
  name: "String", # required
  versions: ["VersionName"], # required
  force: false,
})

Response structure


resp.errors #=> Array
resp.errors[0].version_name #=> String
resp.errors[0].message #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The name of the annotation store from which versions are being deleted.

  • :versions (required, Array<String>) —

    The versions of an annotation store to be deleted.

  • :force (Boolean) —

    Forces the deletion of an annotation store version when imports are in-progress..

Returns:

See Also:



1855
1856
1857
1858
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1855

def delete_annotation_store_versions(params = {}, options = {})
  req = build_request(:delete_annotation_store_versions, params)
  req.send_request(options)
end

#delete_reference(params = {}) ⇒ Struct

Deletes a genome reference.

Examples:

Request syntax with placeholder values


resp = client.delete_reference({
  id: "ReferenceId", # required
  reference_store_id: "ReferenceStoreId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The reference's ID.

  • :reference_store_id (required, String) —

    The reference's store ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



1881
1882
1883
1884
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1881

def delete_reference(params = {}, options = {})
  req = build_request(:delete_reference, params)
  req.send_request(options)
end

#delete_reference_store(params = {}) ⇒ Struct

Deletes a genome reference store.

Examples:

Request syntax with placeholder values


resp = client.delete_reference_store({
  id: "ReferenceStoreId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The store's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



1903
1904
1905
1906
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1903

def delete_reference_store(params = {}, options = {})
  req = build_request(:delete_reference_store, params)
  req.send_request(options)
end

#delete_run(params = {}) ⇒ Struct

Deletes a run and returns a response with no body if the operation is successful. You can only delete a run that has reached a COMPLETED, FAILED, or CANCELLED stage. A completed run has delivered an output, or was cancelled and resulted in no output. When you delete a run, only the metadata associated with the run is deleted. The run outputs remain in Amazon S3 and logs remain in CloudWatch.

To verify that the workflow is deleted:

  • Use ListRuns to confirm the workflow no longer appears in the list.

  • Use GetRun to verify the workflow cannot be found.

Examples:

Request syntax with placeholder values


resp = client.delete_run({
  id: "RunId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The run's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



1937
1938
1939
1940
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1937

def delete_run(params = {}, options = {})
  req = build_request(:delete_run, params)
  req.send_request(options)
end

#delete_run_cache(params = {}) ⇒ Struct

Deletes a run cache and returns a response with no body if the operation is successful. This action removes the cache metadata stored in the service account, but does not delete the data in Amazon S3. You can access the cache data in Amazon S3, for inspection or to troubleshoot issues. You can remove old cache data using standard S3 Delete operations.

For more information, see Deleting a run cache in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.delete_run_cache({
  id: "RunCacheId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    Run cache identifier for the cache you want to delete.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



1971
1972
1973
1974
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1971

def delete_run_cache(params = {}, options = {})
  req = build_request(:delete_run_cache, params)
  req.send_request(options)
end

#delete_run_group(params = {}) ⇒ Struct

Deletes a run group and returns a response with no body if the operation is successful.

To verify that the run group is deleted:

  • Use ListRunGroups to confirm the workflow no longer appears in the list.

  • Use GetRunGroup to verify the workflow cannot be found.

Examples:

Request syntax with placeholder values


resp = client.delete_run_group({
  id: "RunGroupId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The run group's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



2001
2002
2003
2004
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2001

def delete_run_group(params = {}, options = {})
  req = build_request(:delete_run_group, params)
  req.send_request(options)
end

#delete_s3_access_policy(params = {}) ⇒ Struct

Deletes an access policy for the specified store.

Examples:

Request syntax with placeholder values


resp = client.delete_s3_access_policy({
  s3_access_point_arn: "S3AccessPointArn", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :s3_access_point_arn (required, String) —

    The S3 access point ARN that has the access policy.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



2023
2024
2025
2026
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2023

def delete_s3_access_policy(params = {}, options = {})
  req = build_request(:delete_s3_access_policy, params)
  req.send_request(options)
end

#delete_sequence_store(params = {}) ⇒ Struct

Deletes a sequence store.

Examples:

Request syntax with placeholder values


resp = client.delete_sequence_store({
  id: "SequenceStoreId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The sequence store's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



2045
2046
2047
2048
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2045

def delete_sequence_store(params = {}, options = {})
  req = build_request(:delete_sequence_store, params)
  req.send_request(options)
end

#delete_share(params = {}) ⇒ Types::DeleteShareResponse

Deletes a resource share. If you are the resource owner, the subscriber will no longer have access to the shared resource. If you are the subscriber, this operation deletes your access to the share.

Examples:

Request syntax with placeholder values


resp = client.delete_share({
  share_id: "String", # required
})

Response structure


resp.status #=> String, one of "PENDING", "ACTIVATING", "ACTIVE", "DELETING", "DELETED", "FAILED"

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :share_id (required, String) —

    The ID for the resource share to be deleted.

Returns:

See Also:



2075
2076
2077
2078
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2075

def delete_share(params = {}, options = {})
  req = build_request(:delete_share, params)
  req.send_request(options)
end

#delete_variant_store(params = {}) ⇒ Types::DeleteVariantStoreResponse

Deletes a variant store.

Examples:

Request syntax with placeholder values


resp = client.delete_variant_store({
  name: "String", # required
  force: false,
})

Response structure


resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The store's name.

  • :force (Boolean) —

    Whether to force deletion.

Returns:

See Also:



2107
2108
2109
2110
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2107

def delete_variant_store(params = {}, options = {})
  req = build_request(:delete_variant_store, params)
  req.send_request(options)
end

#delete_workflow(params = {}) ⇒ Struct

Deletes a workflow by specifying its ID. No response is returned if the deletion is successful.

To verify that the workflow is deleted:

  • Use ListWorkflows to confirm the workflow no longer appears in the list.

  • Use GetWorkflow to verify the workflow cannot be found.

Examples:

Request syntax with placeholder values


resp = client.delete_workflow({
  id: "WorkflowId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The workflow's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



2137
2138
2139
2140
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2137

def delete_workflow(params = {}, options = {})
  req = build_request(:delete_workflow, params)
  req.send_request(options)
end

#delete_workflow_version(params = {}) ⇒ Struct

Deletes a workflow version. Deleting a workflow version doesn't affect any ongoing runs that are using the workflow version.

For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.delete_workflow_version({
  workflow_id: "WorkflowId", # required
  version_name: "WorkflowVersionName", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :workflow_id (required, String) —

    The workflow's ID.

  • :version_name (required, String) —

    The workflow version name.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



2171
2172
2173
2174
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2171

def delete_workflow_version(params = {}, options = {})
  req = build_request(:delete_workflow_version, params)
  req.send_request(options)
end

#get_annotation_import_job(params = {}) ⇒ Types::GetAnnotationImportResponse

Gets information about an annotation import job.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • annotation_import_job_created

Examples:

Request syntax with placeholder values


resp = client.get_annotation_import_job({
  job_id: "ResourceId", # required
})

Response structure


resp.id #=> String
resp.destination_name #=> String
resp.version_name #=> String
resp.role_arn #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLED", "COMPLETED", "FAILED", "COMPLETED_WITH_FAILURES"
resp.status_message #=> String
resp.creation_time #=> Time
resp.update_time #=> Time
resp.completion_time #=> Time
resp.items #=> Array
resp.items[0].source #=> String
resp.items[0].job_status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLED", "COMPLETED", "FAILED", "COMPLETED_WITH_FAILURES"
resp.run_left_normalization #=> Boolean
resp.format_options.tsv_options.read_options.sep #=> String
resp.format_options.tsv_options.read_options.encoding #=> String
resp.format_options.tsv_options.read_options.quote #=> String
resp.format_options.tsv_options.read_options.quote_all #=> Boolean
resp.format_options.tsv_options.read_options.escape #=> String
resp.format_options.tsv_options.read_options.escape_quotes #=> Boolean
resp.format_options.tsv_options.read_options.comment #=> String
resp.format_options.tsv_options.read_options.header #=> Boolean
resp.format_options.tsv_options.read_options.line_sep #=> String
resp.format_options.vcf_options.ignore_qual_field #=> Boolean
resp.format_options.vcf_options.ignore_filter_field #=> Boolean
resp.annotation_fields #=> Hash
resp.annotation_fields["AnnotationFieldMapKeyString"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :job_id (required, String) —

    The job's ID.

Returns:

See Also:



2241
2242
2243
2244
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2241

def get_annotation_import_job(params = {}, options = {})
  req = build_request(:get_annotation_import_job, params)
  req.send_request(options)
end

#get_annotation_store(params = {}) ⇒ Types::GetAnnotationStoreResponse

Gets information about an annotation store.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • annotation_store_created
  • annotation_store_deleted

Examples:

Request syntax with placeholder values


resp = client.get_annotation_store({
  name: "String", # required
})

Response structure


resp.id #=> String
resp.reference.reference_arn #=> String
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.store_arn #=> String
resp.name #=> String
resp.description #=> String
resp.sse_config.type #=> String, one of "KMS"
resp.sse_config.key_arn #=> String
resp.creation_time #=> Time
resp.update_time #=> Time
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.store_options.tsv_store_options.annotation_type #=> String, one of "GENERIC", "CHR_POS", "CHR_POS_REF_ALT", "CHR_START_END_ONE_BASE", "CHR_START_END_REF_ALT_ONE_BASE", "CHR_START_END_ZERO_BASE", "CHR_START_END_REF_ALT_ZERO_BASE"
resp.store_options.tsv_store_options.format_to_header #=> Hash
resp.store_options.tsv_store_options.format_to_header["FormatToHeaderKey"] #=> String
resp.store_options.tsv_store_options.schema #=> Array
resp.store_options.tsv_store_options.schema[0] #=> Hash
resp.store_options.tsv_store_options.schema[0]["SchemaItemKeyString"] #=> String, one of "LONG", "INT", "STRING", "FLOAT", "DOUBLE", "BOOLEAN"
resp.store_format #=> String, one of "GFF", "TSV", "VCF"
resp.status_message #=> String
resp.store_size_bytes #=> Integer
resp.num_versions #=> Integer

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The store's name.

Returns:

See Also:



2310
2311
2312
2313
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2310

def get_annotation_store(params = {}, options = {})
  req = build_request(:get_annotation_store, params)
  req.send_request(options)
end

#get_annotation_store_version(params = {}) ⇒ Types::GetAnnotationStoreVersionResponse

Retrieves the metadata for an annotation store version.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • annotation_store_version_created
  • annotation_store_version_deleted

Examples:

Request syntax with placeholder values


resp = client.get_annotation_store_version({
  name: "String", # required
  version_name: "String", # required
})

Response structure


resp.store_id #=> String
resp.id #=> String
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.version_arn #=> String
resp.name #=> String
resp.version_name #=> String
resp.description #=> String
resp.creation_time #=> Time
resp.update_time #=> Time
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.version_options.tsv_version_options.annotation_type #=> String, one of "GENERIC", "CHR_POS", "CHR_POS_REF_ALT", "CHR_START_END_ONE_BASE", "CHR_START_END_REF_ALT_ONE_BASE", "CHR_START_END_ZERO_BASE", "CHR_START_END_REF_ALT_ZERO_BASE"
resp.version_options.tsv_version_options.format_to_header #=> Hash
resp.version_options.tsv_version_options.format_to_header["FormatToHeaderKey"] #=> String
resp.version_options.tsv_version_options.schema #=> Array
resp.version_options.tsv_version_options.schema[0] #=> Hash
resp.version_options.tsv_version_options.schema[0]["SchemaItemKeyString"] #=> String, one of "LONG", "INT", "STRING", "FLOAT", "DOUBLE", "BOOLEAN"
resp.status_message #=> String
resp.version_size_bytes #=> Integer

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The name given to an annotation store version to distinguish it from others.

  • :version_name (required, String) —

    The name given to an annotation store version to distinguish it from others.

Returns:

See Also:



2380
2381
2382
2383
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2380

def get_annotation_store_version(params = {}, options = {})
  req = build_request(:get_annotation_store_version, params)
  req.send_request(options)
end

#get_read_set(params = {}) ⇒ Types::GetReadSetResponse

Gets a file from a read set.

Examples:

Request syntax with placeholder values


resp = client.get_read_set({
  id: "ReadSetId", # required
  sequence_store_id: "SequenceStoreId", # required
  file: "SOURCE1", # accepts SOURCE1, SOURCE2, INDEX
  part_number: 1, # required
})

Response structure


resp.payload #=> IO

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The read set's ID.

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :file (String) —

    The file to retrieve.

  • :part_number (required, Integer) —

    The part number to retrieve.

Returns:

See Also:



2420
2421
2422
2423
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2420

def get_read_set(params = {}, options = {}, &block)
  req = build_request(:get_read_set, params)
  req.send_request(options, &block)
end

#get_read_set_activation_job(params = {}) ⇒ Types::GetReadSetActivationJobResponse

Gets information about a read set activation job.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • read_set_activation_job_completed

Examples:

Request syntax with placeholder values


resp = client.get_read_set_activation_job({
  id: "ActivationJobId", # required
  sequence_store_id: "SequenceStoreId", # required
})

Response structure


resp.id #=> String
resp.sequence_store_id #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.status_message #=> String
resp.creation_time #=> Time
resp.completion_time #=> Time
resp.sources #=> Array
resp.sources[0].read_set_id #=> String
resp.sources[0].status #=> String, one of "NOT_STARTED", "IN_PROGRESS", "FINISHED", "FAILED"
resp.sources[0].status_message #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The job's ID.

  • :sequence_store_id (required, String) —

    The job's sequence store ID.

Returns:

See Also:



2472
2473
2474
2475
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2472

def get_read_set_activation_job(params = {}, options = {})
  req = build_request(:get_read_set_activation_job, params)
  req.send_request(options)
end

#get_read_set_export_job(params = {}) ⇒ Types::GetReadSetExportJobResponse

Gets information about a read set export job.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • read_set_export_job_completed

Examples:

Request syntax with placeholder values


resp = client.get_read_set_export_job({
  sequence_store_id: "SequenceStoreId", # required
  id: "ExportJobId", # required
})

Response structure


resp.id #=> String
resp.sequence_store_id #=> String
resp.destination #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.status_message #=> String
resp.creation_time #=> Time
resp.completion_time #=> Time
resp.read_sets #=> Array
resp.read_sets[0].id #=> String
resp.read_sets[0].status #=> String, one of "NOT_STARTED", "IN_PROGRESS", "FINISHED", "FAILED"
resp.read_sets[0].status_message #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The job's sequence store ID.

  • :id (required, String) —

    The job's ID.

Returns:

See Also:



2526
2527
2528
2529
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2526

def get_read_set_export_job(params = {}, options = {})
  req = build_request(:get_read_set_export_job, params)
  req.send_request(options)
end

#get_read_set_import_job(params = {}) ⇒ Types::GetReadSetImportJobResponse

Gets information about a read set import job.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • read_set_import_job_completed

Examples:

Request syntax with placeholder values


resp = client.get_read_set_import_job({
  id: "ImportJobId", # required
  sequence_store_id: "SequenceStoreId", # required
})

Response structure


resp.id #=> String
resp.sequence_store_id #=> String
resp.role_arn #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.status_message #=> String
resp.creation_time #=> Time
resp.completion_time #=> Time
resp.sources #=> Array
resp.sources[0].source_files.source1 #=> String
resp.sources[0].source_files.source2 #=> String
resp.sources[0].source_file_type #=> String, one of "FASTQ", "BAM", "CRAM", "UBAM"
resp.sources[0].status #=> String, one of "NOT_STARTED", "IN_PROGRESS", "FINISHED", "FAILED"
resp.sources[0].status_message #=> String
resp.sources[0].subject_id #=> String
resp.sources[0].sample_id #=> String
resp.sources[0].generated_from #=> String
resp.sources[0].reference_arn #=> String
resp.sources[0].name #=> String
resp.sources[0].description #=> String
resp.sources[0].tags #=> Hash
resp.sources[0].tags["TagKey"] #=> String
resp.sources[0].read_set_id #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The job's ID.

  • :sequence_store_id (required, String) —

    The job's sequence store ID.

Returns:

See Also:



2591
2592
2593
2594
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2591

def get_read_set_import_job(params = {}, options = {})
  req = build_request(:get_read_set_import_job, params)
  req.send_request(options)
end

#get_read_set_metadata(params = {}) ⇒ Types::GetReadSetMetadataResponse

Gets details about a read set.

Examples:

Request syntax with placeholder values


resp = client.get_read_set_metadata({
  id: "ReadSetId", # required
  sequence_store_id: "SequenceStoreId", # required
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.sequence_store_id #=> String
resp.subject_id #=> String
resp.sample_id #=> String
resp.status #=> String, one of "ARCHIVED", "ACTIVATING", "ACTIVE", "DELETING", "DELETED", "PROCESSING_UPLOAD", "UPLOAD_FAILED"
resp.name #=> String
resp.description #=> String
resp.file_type #=> String, one of "FASTQ", "BAM", "CRAM", "UBAM"
resp.creation_time #=> Time
resp.sequence_information.total_read_count #=> Integer
resp.sequence_information.total_base_count #=> Integer
resp.sequence_information.generated_from #=> String
resp.sequence_information.alignment #=> String
resp.reference_arn #=> String
resp.files.source1.total_parts #=> Integer
resp.files.source1.part_size #=> Integer
resp.files.source1.content_length #=> Integer
resp.files.source1.s3_access.s3_uri #=> String
resp.files.source2.total_parts #=> Integer
resp.files.source2.part_size #=> Integer
resp.files.source2.content_length #=> Integer
resp.files.source2.s3_access.s3_uri #=> String
resp.files.index.total_parts #=> Integer
resp.files.index.part_size #=> Integer
resp.files.index.content_length #=> Integer
resp.files.index.s3_access.s3_uri #=> String
resp.status_message #=> String
resp.creation_type #=> String, one of "IMPORT", "UPLOAD"
resp.etag.algorithm #=> String, one of "FASTQ_MD5up", "BAM_MD5up", "CRAM_MD5up", "FASTQ_SHA256up", "BAM_SHA256up", "CRAM_SHA256up", "FASTQ_SHA512up", "BAM_SHA512up", "CRAM_SHA512up"
resp.etag.source1 #=> String
resp.etag.source2 #=> String
resp.creation_job_id #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The read set's ID.

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

Returns:

See Also:



2671
2672
2673
2674
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2671

def get_read_set_metadata(params = {}, options = {})
  req = build_request(:get_read_set_metadata, params)
  req.send_request(options)
end

#get_reference(params = {}) ⇒ Types::GetReferenceResponse

Gets a reference file.

Examples:

Request syntax with placeholder values


resp = client.get_reference({
  id: "ReferenceId", # required
  reference_store_id: "ReferenceStoreId", # required
  range: "Range",
  part_number: 1, # required
  file: "SOURCE", # accepts SOURCE, INDEX
})

Response structure


resp.payload #=> IO

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The reference's ID.

  • :reference_store_id (required, String) —

    The reference's store ID.

  • :range (String) —

    The range to retrieve.

  • :part_number (required, Integer) —

    The part number to retrieve.

  • :file (String) —

    The file to retrieve.

Returns:

See Also:



2715
2716
2717
2718
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2715

def get_reference(params = {}, options = {}, &block)
  req = build_request(:get_reference, params)
  req.send_request(options, &block)
end

#get_reference_import_job(params = {}) ⇒ Types::GetReferenceImportJobResponse

Gets information about a reference import job.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • reference_import_job_completed

Examples:

Request syntax with placeholder values


resp = client.get_reference_import_job({
  id: "ImportJobId", # required
  reference_store_id: "ReferenceStoreId", # required
})

Response structure


resp.id #=> String
resp.reference_store_id #=> String
resp.role_arn #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.status_message #=> String
resp.creation_time #=> Time
resp.completion_time #=> Time
resp.sources #=> Array
resp.sources[0].source_file #=> String
resp.sources[0].status #=> String, one of "NOT_STARTED", "IN_PROGRESS", "FINISHED", "FAILED"
resp.sources[0].status_message #=> String
resp.sources[0].name #=> String
resp.sources[0].description #=> String
resp.sources[0].tags #=> Hash
resp.sources[0].tags["TagKey"] #=> String
resp.sources[0].reference_id #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The job's ID.

  • :reference_store_id (required, String) —

    The job's reference store ID.

Returns:

See Also:



2774
2775
2776
2777
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2774

def get_reference_import_job(params = {}, options = {})
  req = build_request(:get_reference_import_job, params)
  req.send_request(options)
end

#get_reference_metadata(params = {}) ⇒ Types::GetReferenceMetadataResponse

Gets information about a genome reference's metadata.

Examples:

Request syntax with placeholder values


resp = client.get_reference_metadata({
  id: "ReferenceId", # required
  reference_store_id: "ReferenceStoreId", # required
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.reference_store_id #=> String
resp.md5 #=> String
resp.status #=> String, one of "ACTIVE", "DELETING", "DELETED"
resp.name #=> String
resp.description #=> String
resp.creation_time #=> Time
resp.update_time #=> Time
resp.files.source.total_parts #=> Integer
resp.files.source.part_size #=> Integer
resp.files.source.content_length #=> Integer
resp.files.source.s3_access.s3_uri #=> String
resp.files.index.total_parts #=> Integer
resp.files.index.part_size #=> Integer
resp.files.index.content_length #=> Integer
resp.files.index.s3_access.s3_uri #=> String
resp.creation_type #=> String, one of "IMPORT"
resp.creation_job_id #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The reference's ID.

  • :reference_store_id (required, String) —

    The reference's reference store ID.

Returns:

See Also:



2835
2836
2837
2838
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2835

def get_reference_metadata(params = {}, options = {})
  req = build_request(:get_reference_metadata, params)
  req.send_request(options)
end

#get_reference_store(params = {}) ⇒ Types::GetReferenceStoreResponse

Gets information about a reference store.

Examples:

Request syntax with placeholder values


resp = client.get_reference_store({
  id: "ReferenceStoreId", # required
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.name #=> String
resp.description #=> String
resp.sse_config.type #=> String, one of "KMS"
resp.sse_config.key_arn #=> String
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The store's ID.

Returns:

See Also:



2874
2875
2876
2877
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2874

def get_reference_store(params = {}, options = {})
  req = build_request(:get_reference_store, params)
  req.send_request(options)
end

#get_run(params = {}) ⇒ Types::GetRunResponse

Gets detailed information about a specific run using its ID.

Amazon Web Services HealthOmics stores a configurable number of runs, as determined by service limits, that are available to the console and API. If GetRun does not return the requested run, you can find all run logs in the CloudWatch logs. For more information about viewing the run logs, see CloudWatch logs in the Amazon Web Services HealthOmics User Guide.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • run_completed
  • run_running

Examples:

Request syntax with placeholder values


resp = client.get_run({
  id: "RunId", # required
  export: ["DEFINITION"], # accepts DEFINITION
})

Response structure


resp.arn #=> String
resp.id #=> String
resp.cache_id #=> String
resp.cache_behavior #=> String, one of "CACHE_ON_FAILURE", "CACHE_ALWAYS"
resp.engine_version #=> String
resp.status #=> String, one of "PENDING", "STARTING", "RUNNING", "STOPPING", "COMPLETED", "DELETED", "CANCELLED", "FAILED"
resp.workflow_id #=> String
resp.workflow_type #=> String, one of "PRIVATE", "READY2RUN"
resp.run_id #=> String
resp.role_arn #=> String
resp.name #=> String
resp.run_group_id #=> String
resp.priority #=> Integer
resp.definition #=> String
resp.digest #=> String
resp.storage_capacity #=> Integer
resp.output_uri #=> String
resp.log_level #=> String, one of "OFF", "FATAL", "ERROR", "ALL"
resp.resource_digests #=> Hash
resp.resource_digests["RunResourceDigestKey"] #=> String
resp.started_by #=> String
resp.creation_time #=> Time
resp.start_time #=> Time
resp.stop_time #=> Time
resp.status_message #=> String
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.accelerators #=> String, one of "GPU"
resp.retention_mode #=> String, one of "RETAIN", "REMOVE"
resp.failure_reason #=> String
resp.log_location.engine_log_stream #=> String
resp.log_location.run_log_stream #=> String
resp.uuid #=> String
resp.run_output_uri #=> String
resp.storage_type #=> String, one of "STATIC", "DYNAMIC"
resp.workflow_owner_id #=> String
resp.workflow_version_name #=> String
resp.workflow_uuid #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The run's ID.

  • :export (Array<String>) —

    The run's export format.

Returns:

See Also:



2995
2996
2997
2998
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2995

def get_run(params = {}, options = {})
  req = build_request(:get_run, params)
  req.send_request(options)
end

#get_run_cache(params = {}) ⇒ Types::GetRunCacheResponse

Retrieves detailed information about the specified run cache using its ID.

For more information, see Call caching for Amazon Web Services HealthOmics runs in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.get_run_cache({
  id: "RunCacheId", # required
})

Response structure


resp.arn #=> String
resp.cache_behavior #=> String, one of "CACHE_ON_FAILURE", "CACHE_ALWAYS"
resp.cache_bucket_owner_id #=> String
resp.cache_s3_uri #=> String
resp.creation_time #=> Time
resp.description #=> String
resp.id #=> String
resp.name #=> String
resp.status #=> String, one of "ACTIVE", "DELETED", "FAILED"
resp.tags #=> Hash
resp.tags["TagKey"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The identifier of the run cache to retrieve.

Returns:

See Also:



3051
3052
3053
3054
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3051

def get_run_cache(params = {}, options = {})
  req = build_request(:get_run_cache, params)
  req.send_request(options)
end

#get_run_group(params = {}) ⇒ Types::GetRunGroupResponse

Gets information about a run group and returns its metadata.

Examples:

Request syntax with placeholder values


resp = client.get_run_group({
  id: "RunGroupId", # required
})

Response structure


resp.arn #=> String
resp.id #=> String
resp.name #=> String
resp.max_cpus #=> Integer
resp.max_runs #=> Integer
resp.max_duration #=> Integer
resp.creation_time #=> Time
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.max_gpus #=> Integer

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The group's ID.

Returns:

See Also:



3096
3097
3098
3099
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3096

def get_run_group(params = {}, options = {})
  req = build_request(:get_run_group, params)
  req.send_request(options)
end

#get_run_task(params = {}) ⇒ Types::GetRunTaskResponse

Gets detailed information about a run task using its ID.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • task_completed
  • task_running

Examples:

Request syntax with placeholder values


resp = client.get_run_task({
  id: "RunId", # required
  task_id: "TaskId", # required
})

Response structure


resp.task_id #=> String
resp.status #=> String, one of "PENDING", "STARTING", "RUNNING", "STOPPING", "COMPLETED", "CANCELLED", "FAILED"
resp.name #=> String
resp.cpus #=> Integer
resp.cache_hit #=> Boolean
resp.cache_s3_uri #=> String
resp.memory #=> Integer
resp.creation_time #=> Time
resp.start_time #=> Time
resp.stop_time #=> Time
resp.status_message #=> String
resp.log_stream #=> String
resp.gpus #=> Integer
resp.instance_type #=> String
resp.failure_reason #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The workflow run ID.

  • :task_id (required, String) —

    The task's ID.

Returns:

See Also:



3162
3163
3164
3165
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3162

def get_run_task(params = {}, options = {})
  req = build_request(:get_run_task, params)
  req.send_request(options)
end

#get_s3_access_policy(params = {}) ⇒ Types::GetS3AccessPolicyResponse

Retrieves details about an access policy on a given store.

Examples:

Request syntax with placeholder values


resp = client.get_s3_access_policy({
  s3_access_point_arn: "S3AccessPointArn", # required
})

Response structure


resp.s3_access_point_arn #=> String
resp.store_id #=> String
resp.store_type #=> String, one of "SEQUENCE_STORE", "REFERENCE_STORE"
resp.update_time #=> Time
resp.s3_access_policy #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :s3_access_point_arn (required, String) —

    The S3 access point ARN that has the access policy.

Returns:

See Also:



3198
3199
3200
3201
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3198

def get_s3_access_policy(params = {}, options = {})
  req = build_request(:get_s3_access_policy, params)
  req.send_request(options)
end

#get_sequence_store(params = {}) ⇒ Types::GetSequenceStoreResponse

Gets information about a sequence store.

Examples:

Request syntax with placeholder values


resp = client.get_sequence_store({
  id: "SequenceStoreId", # required
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.name #=> String
resp.description #=> String
resp.sse_config.type #=> String, one of "KMS"
resp.sse_config.key_arn #=> String
resp.creation_time #=> Time
resp.fallback_location #=> String
resp.s3_access.s3_uri #=> String
resp.s3_access.s3_access_point_arn #=> String
resp.s3_access.access_log_location #=> String
resp.e_tag_algorithm_family #=> String, one of "MD5up", "SHA256up", "SHA512up"
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETING", "FAILED"
resp.status_message #=> String
resp.propagated_set_level_tags #=> Array
resp.propagated_set_level_tags[0] #=> String
resp.update_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The store's ID.

Returns:

See Also:



3254
3255
3256
3257
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3254

def get_sequence_store(params = {}, options = {})
  req = build_request(:get_sequence_store, params)
  req.send_request(options)
end

#get_share(params = {}) ⇒ Types::GetShareResponse

Retrieves the metadata for the specified resource share.

Examples:

Request syntax with placeholder values


resp = client.get_share({
  share_id: "String", # required
})

Response structure


resp.share.share_id #=> String
resp.share.resource_arn #=> String
resp.share.resource_id #=> String
resp.share.principal_subscriber #=> String
resp.share.owner_id #=> String
resp.share.status #=> String, one of "PENDING", "ACTIVATING", "ACTIVE", "DELETING", "DELETED", "FAILED"
resp.share.status_message #=> String
resp.share.share_name #=> String
resp.share.creation_time #=> Time
resp.share.update_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :share_id (required, String) —

    The ID of the share.

Returns:

See Also:



3291
3292
3293
3294
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3291

def get_share(params = {}, options = {})
  req = build_request(:get_share, params)
  req.send_request(options)
end

#get_variant_import_job(params = {}) ⇒ Types::GetVariantImportResponse

Gets information about a variant import job.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • variant_import_job_created

Examples:

Request syntax with placeholder values


resp = client.get_variant_import_job({
  job_id: "ResourceId", # required
})

Response structure


resp.id #=> String
resp.destination_name #=> String
resp.role_arn #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLED", "COMPLETED", "FAILED", "COMPLETED_WITH_FAILURES"
resp.status_message #=> String
resp.creation_time #=> Time
resp.update_time #=> Time
resp.completion_time #=> Time
resp.items #=> Array
resp.items[0].source #=> String
resp.items[0].job_status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLED", "COMPLETED", "FAILED", "COMPLETED_WITH_FAILURES"
resp.items[0].status_message #=> String
resp.run_left_normalization #=> Boolean
resp.annotation_fields #=> Hash
resp.annotation_fields["AnnotationFieldMapKeyString"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :job_id (required, String) —

    The job's ID.

Returns:

See Also:



3348
3349
3350
3351
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3348

def get_variant_import_job(params = {}, options = {})
  req = build_request(:get_variant_import_job, params)
  req.send_request(options)
end

#get_variant_store(params = {}) ⇒ Types::GetVariantStoreResponse

Gets information about a variant store.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • variant_store_created
  • variant_store_deleted

Examples:

Request syntax with placeholder values


resp = client.get_variant_store({
  name: "String", # required
})

Response structure


resp.id #=> String
resp.reference.reference_arn #=> String
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.store_arn #=> String
resp.name #=> String
resp.description #=> String
resp.sse_config.type #=> String, one of "KMS"
resp.sse_config.key_arn #=> String
resp.creation_time #=> Time
resp.update_time #=> Time
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.status_message #=> String
resp.store_size_bytes #=> Integer

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The store's name.

Returns:

See Also:



3406
3407
3408
3409
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3406

def get_variant_store(params = {}, options = {})
  req = build_request(:get_variant_store, params)
  req.send_request(options)
end

#get_workflow(params = {}) ⇒ Types::GetWorkflowResponse

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.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • workflow_active

Examples:

Request syntax with placeholder values


resp = client.get_workflow({
  id: "WorkflowId", # required
  type: "PRIVATE", # accepts PRIVATE, READY2RUN
  export: ["DEFINITION"], # accepts DEFINITION, README
  workflow_owner_id: "WorkflowOwnerId",
})

Response structure


resp.arn #=> String
resp.id #=> String
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETED", "FAILED", "INACTIVE"
resp.type #=> String, one of "PRIVATE", "READY2RUN"
resp.name #=> String
resp.description #=> String
resp.engine #=> String, one of "WDL", "NEXTFLOW", "CWL"
resp.definition #=> String
resp.main #=> String
resp.digest #=> String
resp.parameter_template #=> Hash
resp.parameter_template["WorkflowParameterName"].description #=> String
resp.parameter_template["WorkflowParameterName"].optional #=> Boolean
resp.storage_capacity #=> Integer
resp.creation_time #=> Time
resp.status_message #=> String
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.metadata #=> Hash
resp.metadata["WorkflowMetadataKey"] #=> String
resp.accelerators #=> String, one of "GPU"
resp.storage_type #=> String, one of "STATIC", "DYNAMIC"
resp.uuid #=> String
resp.readme #=> String
resp.definition_repository_details.connection_arn #=> String
resp.definition_repository_details.full_repository_id #=> String
resp.definition_repository_details.source_reference.type #=> String, one of "BRANCH", "TAG", "COMMIT"
resp.definition_repository_details.source_reference.value #=> String
resp.definition_repository_details.provider_type #=> String
resp.definition_repository_details.provider_endpoint #=> String
resp.readme_path #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The workflow's ID.

  • :type (String) —

    The workflow's type.

  • :export (Array<String>) —

    The export format for the workflow.

  • :workflow_owner_id (String) —

    The ID of the workflow owner.

Returns:

See Also:



3512
3513
3514
3515
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3512

def get_workflow(params = {}, options = {})
  req = build_request(:get_workflow, params)
  req.send_request(options)
end

#get_workflow_version(params = {}) ⇒ Types::GetWorkflowVersionResponse

Gets information about a workflow version. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.

The following waiters are defined for this operation (see #wait_until for detailed usage):

  • workflow_version_active

Examples:

Request syntax with placeholder values


resp = client.get_workflow_version({
  workflow_id: "WorkflowId", # required
  version_name: "WorkflowVersionName", # required
  type: "PRIVATE", # accepts PRIVATE, READY2RUN
  export: ["DEFINITION"], # accepts DEFINITION, README
  workflow_owner_id: "WorkflowOwnerId",
})

Response structure


resp.arn #=> String
resp.workflow_id #=> String
resp.version_name #=> String
resp.accelerators #=> String, one of "GPU"
resp.creation_time #=> Time
resp.description #=> String
resp.definition #=> String
resp.digest #=> String
resp.engine #=> String, one of "WDL", "NEXTFLOW", "CWL"
resp.main #=> String
resp.metadata #=> Hash
resp.metadata["WorkflowMetadataKey"] #=> String
resp.parameter_template #=> Hash
resp.parameter_template["WorkflowParameterName"].description #=> String
resp.parameter_template["WorkflowParameterName"].optional #=> Boolean
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETED", "FAILED", "INACTIVE"
resp.status_message #=> String
resp.storage_type #=> String, one of "STATIC", "DYNAMIC"
resp.storage_capacity #=> Integer
resp.type #=> String, one of "PRIVATE", "READY2RUN"
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.uuid #=> String
resp.workflow_bucket_owner_id #=> String
resp.readme #=> String
resp.definition_repository_details.connection_arn #=> String
resp.definition_repository_details.full_repository_id #=> String
resp.definition_repository_details.source_reference.type #=> String, one of "BRANCH", "TAG", "COMMIT"
resp.definition_repository_details.source_reference.value #=> String
resp.definition_repository_details.provider_type #=> String
resp.definition_repository_details.provider_endpoint #=> String
resp.readme_path #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :workflow_id (required, String) —

    The workflow's ID.

  • :version_name (required, String) —

    The workflow version name.

  • :type (String) —

    The workflow's type.

  • :export (Array<String>) —

    The export format for the workflow.

  • :workflow_owner_id (String) —

    Amazon Web Services Id of the owner of the workflow.

Returns:

See Also:



3620
3621
3622
3623
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3620

def get_workflow_version(params = {}, options = {})
  req = build_request(:get_workflow_version, params)
  req.send_request(options)
end

#list_annotation_import_jobs(params = {}) ⇒ Types::ListAnnotationImportJobsResponse

Retrieves a list of annotation import jobs.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_annotation_import_jobs({
  max_results: 1,
  ids: ["ResourceIdentifier"],
  next_token: "ListAnnotationImportJobsRequestNextTokenString",
  filter: {
    status: "SUBMITTED", # accepts SUBMITTED, IN_PROGRESS, CANCELLED, COMPLETED, FAILED, COMPLETED_WITH_FAILURES
    store_name: "String",
  },
})

Response structure


resp.annotation_import_jobs #=> Array
resp.annotation_import_jobs[0].id #=> String
resp.annotation_import_jobs[0].destination_name #=> String
resp.annotation_import_jobs[0].version_name #=> String
resp.annotation_import_jobs[0].role_arn #=> String
resp.annotation_import_jobs[0].status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLED", "COMPLETED", "FAILED", "COMPLETED_WITH_FAILURES"
resp.annotation_import_jobs[0].creation_time #=> Time
resp.annotation_import_jobs[0].update_time #=> Time
resp.annotation_import_jobs[0].completion_time #=> Time
resp.annotation_import_jobs[0].run_left_normalization #=> Boolean
resp.annotation_import_jobs[0].annotation_fields #=> Hash
resp.annotation_import_jobs[0].annotation_fields["AnnotationFieldMapKeyString"] #=> String
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :ids (Array<String>) —

    IDs of annotation import jobs to retrieve.

  • :next_token (String) —

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

  • :filter (Types::ListAnnotationImportJobsFilter) —

    A filter to apply to the list.

Returns:

See Also:



3679
3680
3681
3682
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3679

def list_annotation_import_jobs(params = {}, options = {})
  req = build_request(:list_annotation_import_jobs, params)
  req.send_request(options)
end

#list_annotation_store_versions(params = {}) ⇒ Types::ListAnnotationStoreVersionsResponse

Lists the versions of an annotation store.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_annotation_store_versions({
  name: "String", # required
  max_results: 1,
  next_token: "ListAnnotationStoreVersionsRequestNextTokenString",
  filter: {
    status: "CREATING", # accepts CREATING, UPDATING, DELETING, ACTIVE, FAILED
  },
})

Response structure


resp.annotation_store_versions #=> Array
resp.annotation_store_versions[0].store_id #=> String
resp.annotation_store_versions[0].id #=> String
resp.annotation_store_versions[0].status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.annotation_store_versions[0].version_arn #=> String
resp.annotation_store_versions[0].name #=> String
resp.annotation_store_versions[0].version_name #=> String
resp.annotation_store_versions[0].description #=> String
resp.annotation_store_versions[0].creation_time #=> Time
resp.annotation_store_versions[0].update_time #=> Time
resp.annotation_store_versions[0].status_message #=> String
resp.annotation_store_versions[0].version_size_bytes #=> Integer
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The name of an annotation store.

  • :max_results (Integer) —

    The maximum number of annotation store versions to return in one page of results.

  • :next_token (String) —

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

  • :filter (Types::ListAnnotationStoreVersionsFilter) —

    A filter to apply to the list of annotation store versions.

Returns:

See Also:



3738
3739
3740
3741
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3738

def list_annotation_store_versions(params = {}, options = {})
  req = build_request(:list_annotation_store_versions, params)
  req.send_request(options)
end

#list_annotation_stores(params = {}) ⇒ Types::ListAnnotationStoresResponse

Retrieves a list of annotation stores.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_annotation_stores({
  ids: ["ResourceIdentifier"],
  max_results: 1,
  next_token: "ListAnnotationStoresRequestNextTokenString",
  filter: {
    status: "CREATING", # accepts CREATING, UPDATING, DELETING, ACTIVE, FAILED
  },
})

Response structure


resp.annotation_stores #=> Array
resp.annotation_stores[0].id #=> String
resp.annotation_stores[0].reference.reference_arn #=> String
resp.annotation_stores[0].status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.annotation_stores[0].store_arn #=> String
resp.annotation_stores[0].name #=> String
resp.annotation_stores[0].store_format #=> String, one of "GFF", "TSV", "VCF"
resp.annotation_stores[0].description #=> String
resp.annotation_stores[0].sse_config.type #=> String, one of "KMS"
resp.annotation_stores[0].sse_config.key_arn #=> String
resp.annotation_stores[0].creation_time #=> Time
resp.annotation_stores[0].update_time #=> Time
resp.annotation_stores[0].status_message #=> String
resp.annotation_stores[0].store_size_bytes #=> Integer
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :ids (Array<String>) —

    IDs of stores to list.

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ListAnnotationStoresFilter) —

    A filter to apply to the list.

Returns:

See Also:



3798
3799
3800
3801
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3798

def list_annotation_stores(params = {}, options = {})
  req = build_request(:list_annotation_stores, params)
  req.send_request(options)
end

#list_multipart_read_set_uploads(params = {}) ⇒ Types::ListMultipartReadSetUploadsResponse

Lists multipart read set uploads and for in progress uploads. Once the upload is completed, a read set is created and the upload will no longer be returned in the response.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_multipart_read_set_uploads({
  sequence_store_id: "SequenceStoreId", # required
  max_results: 1,
  next_token: "NextToken",
})

Response structure


resp.next_token #=> String
resp.uploads #=> Array
resp.uploads[0].sequence_store_id #=> String
resp.uploads[0].upload_id #=> String
resp.uploads[0].source_file_type #=> String, one of "FASTQ", "BAM", "CRAM", "UBAM"
resp.uploads[0].subject_id #=> String
resp.uploads[0].sample_id #=> String
resp.uploads[0].generated_from #=> String
resp.uploads[0].reference_arn #=> String
resp.uploads[0].name #=> String
resp.uploads[0].description #=> String
resp.uploads[0].tags #=> Hash
resp.uploads[0].tags["TagKey"] #=> String
resp.uploads[0].creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The Sequence Store ID used for the multipart uploads.

  • :max_results (Integer) —

    The maximum number of multipart uploads returned in a page.

  • :next_token (String) —

    Next token returned in the response of a previous ListMultipartReadSetUploads call. Used to get the next page of results.

Returns:

See Also:



3854
3855
3856
3857
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3854

def list_multipart_read_set_uploads(params = {}, options = {})
  req = build_request(:list_multipart_read_set_uploads, params)
  req.send_request(options)
end

#list_read_set_activation_jobs(params = {}) ⇒ Types::ListReadSetActivationJobsResponse

Retrieves a list of read set activation jobs.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_read_set_activation_jobs({
  sequence_store_id: "SequenceStoreId", # required
  max_results: 1,
  next_token: "NextToken",
  filter: {
    status: "SUBMITTED", # accepts SUBMITTED, IN_PROGRESS, CANCELLING, CANCELLED, FAILED, COMPLETED, COMPLETED_WITH_FAILURES
    created_after: Time.now,
    created_before: Time.now,
  },
})

Response structure


resp.next_token #=> String
resp.activation_jobs #=> Array
resp.activation_jobs[0].id #=> String
resp.activation_jobs[0].sequence_store_id #=> String
resp.activation_jobs[0].status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.activation_jobs[0].creation_time #=> Time
resp.activation_jobs[0].completion_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :max_results (Integer) —

    The maximum number of read set activation jobs to return in one page of results.

  • :next_token (String) —

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

  • :filter (Types::ActivateReadSetFilter) —

    A filter to apply to the list.

Returns:

See Also:



3909
3910
3911
3912
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3909

def list_read_set_activation_jobs(params = {}, options = {})
  req = build_request(:list_read_set_activation_jobs, params)
  req.send_request(options)
end

#list_read_set_export_jobs(params = {}) ⇒ Types::ListReadSetExportJobsResponse

Retrieves a list of read set export jobs.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_read_set_export_jobs({
  sequence_store_id: "SequenceStoreId", # required
  max_results: 1,
  next_token: "NextToken",
  filter: {
    status: "SUBMITTED", # accepts SUBMITTED, IN_PROGRESS, CANCELLING, CANCELLED, FAILED, COMPLETED, COMPLETED_WITH_FAILURES
    created_after: Time.now,
    created_before: Time.now,
  },
})

Response structure


resp.next_token #=> String
resp.export_jobs #=> Array
resp.export_jobs[0].id #=> String
resp.export_jobs[0].sequence_store_id #=> String
resp.export_jobs[0].destination #=> String
resp.export_jobs[0].status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.export_jobs[0].creation_time #=> Time
resp.export_jobs[0].completion_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The jobs' sequence store ID.

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ExportReadSetFilter) —

    A filter to apply to the list.

Returns:

See Also:



3964
3965
3966
3967
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3964

def list_read_set_export_jobs(params = {}, options = {})
  req = build_request(:list_read_set_export_jobs, params)
  req.send_request(options)
end

#list_read_set_import_jobs(params = {}) ⇒ Types::ListReadSetImportJobsResponse

Retrieves a list of read set import jobs.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_read_set_import_jobs({
  max_results: 1,
  next_token: "NextToken",
  sequence_store_id: "SequenceStoreId", # required
  filter: {
    status: "SUBMITTED", # accepts SUBMITTED, IN_PROGRESS, CANCELLING, CANCELLED, FAILED, COMPLETED, COMPLETED_WITH_FAILURES
    created_after: Time.now,
    created_before: Time.now,
  },
})

Response structure


resp.next_token #=> String
resp.import_jobs #=> Array
resp.import_jobs[0].id #=> String
resp.import_jobs[0].sequence_store_id #=> String
resp.import_jobs[0].role_arn #=> String
resp.import_jobs[0].status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.import_jobs[0].creation_time #=> Time
resp.import_jobs[0].completion_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :sequence_store_id (required, String) —

    The jobs' sequence store ID.

  • :filter (Types::ImportReadSetFilter) —

    A filter to apply to the list.

Returns:

See Also:



4019
4020
4021
4022
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4019

def list_read_set_import_jobs(params = {}, options = {})
  req = build_request(:list_read_set_import_jobs, params)
  req.send_request(options)
end

#list_read_set_upload_parts(params = {}) ⇒ Types::ListReadSetUploadPartsResponse

This operation will list all parts in a requested multipart upload for a sequence store.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_read_set_upload_parts({
  sequence_store_id: "SequenceStoreId", # required
  upload_id: "UploadId", # required
  part_source: "SOURCE1", # required, accepts SOURCE1, SOURCE2
  max_results: 1,
  next_token: "NextToken",
  filter: {
    created_after: Time.now,
    created_before: Time.now,
  },
})

Response structure


resp.next_token #=> String
resp.parts #=> Array
resp.parts[0].part_number #=> Integer
resp.parts[0].part_size #=> Integer
resp.parts[0].part_source #=> String, one of "SOURCE1", "SOURCE2"
resp.parts[0].checksum #=> String
resp.parts[0].creation_time #=> Time
resp.parts[0].last_updated_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The Sequence Store ID used for the multipart uploads.

  • :upload_id (required, String) —

    The ID for the initiated multipart upload.

  • :part_source (required, String) —

    The source file for the upload part.

  • :max_results (Integer) —

    The maximum number of read set upload parts returned in a page.

  • :next_token (String) —

    Next token returned in the response of a previous ListReadSetUploadPartsRequest call. Used to get the next page of results.

  • :filter (Types::ReadSetUploadPartListFilter) —

    Attributes used to filter for a specific subset of read set part uploads.

Returns:

See Also:



4084
4085
4086
4087
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4084

def list_read_set_upload_parts(params = {}, options = {})
  req = build_request(:list_read_set_upload_parts, params)
  req.send_request(options)
end

#list_read_sets(params = {}) ⇒ Types::ListReadSetsResponse

Retrieves a list of read sets.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_read_sets({
  sequence_store_id: "SequenceStoreId", # required
  max_results: 1,
  next_token: "NextToken",
  filter: {
    name: "ReadSetName",
    status: "ARCHIVED", # accepts ARCHIVED, ACTIVATING, ACTIVE, DELETING, DELETED, PROCESSING_UPLOAD, UPLOAD_FAILED
    reference_arn: "ReferenceArnFilter",
    created_after: Time.now,
    created_before: Time.now,
    sample_id: "SampleId",
    subject_id: "SubjectId",
    generated_from: "GeneratedFrom",
    creation_type: "IMPORT", # accepts IMPORT, UPLOAD
  },
})

Response structure


resp.next_token #=> String
resp.read_sets #=> Array
resp.read_sets[0].id #=> String
resp.read_sets[0].arn #=> String
resp.read_sets[0].sequence_store_id #=> String
resp.read_sets[0].subject_id #=> String
resp.read_sets[0].sample_id #=> String
resp.read_sets[0].status #=> String, one of "ARCHIVED", "ACTIVATING", "ACTIVE", "DELETING", "DELETED", "PROCESSING_UPLOAD", "UPLOAD_FAILED"
resp.read_sets[0].name #=> String
resp.read_sets[0].description #=> String
resp.read_sets[0].reference_arn #=> String
resp.read_sets[0].file_type #=> String, one of "FASTQ", "BAM", "CRAM", "UBAM"
resp.read_sets[0].sequence_information.total_read_count #=> Integer
resp.read_sets[0].sequence_information.total_base_count #=> Integer
resp.read_sets[0].sequence_information.generated_from #=> String
resp.read_sets[0].sequence_information.alignment #=> String
resp.read_sets[0].creation_time #=> Time
resp.read_sets[0].status_message #=> String
resp.read_sets[0].creation_type #=> String, one of "IMPORT", "UPLOAD"
resp.read_sets[0].etag.algorithm #=> String, one of "FASTQ_MD5up", "BAM_MD5up", "CRAM_MD5up", "FASTQ_SHA256up", "BAM_SHA256up", "CRAM_SHA256up", "FASTQ_SHA512up", "BAM_SHA512up", "CRAM_SHA512up"
resp.read_sets[0].etag.source1 #=> String
resp.read_sets[0].etag.source2 #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The jobs' sequence store ID.

  • :max_results (Integer) —

    The maximum number of read sets to return in one page of results.

  • :next_token (String) —

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

  • :filter (Types::ReadSetFilter) —

    A filter to apply to the list.

Returns:

See Also:



4159
4160
4161
4162
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4159

def list_read_sets(params = {}, options = {})
  req = build_request(:list_read_sets, params)
  req.send_request(options)
end

#list_reference_import_jobs(params = {}) ⇒ Types::ListReferenceImportJobsResponse

Retrieves a list of reference import jobs.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_reference_import_jobs({
  max_results: 1,
  next_token: "NextToken",
  reference_store_id: "ReferenceStoreId", # required
  filter: {
    status: "SUBMITTED", # accepts SUBMITTED, IN_PROGRESS, CANCELLING, CANCELLED, FAILED, COMPLETED, COMPLETED_WITH_FAILURES
    created_after: Time.now,
    created_before: Time.now,
  },
})

Response structure


resp.next_token #=> String
resp.import_jobs #=> Array
resp.import_jobs[0].id #=> String
resp.import_jobs[0].reference_store_id #=> String
resp.import_jobs[0].role_arn #=> String
resp.import_jobs[0].status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.import_jobs[0].creation_time #=> Time
resp.import_jobs[0].completion_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :reference_store_id (required, String) —

    The job's reference store ID.

  • :filter (Types::ImportReferenceFilter) —

    A filter to apply to the list.

Returns:

See Also:



4214
4215
4216
4217
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4214

def list_reference_import_jobs(params = {}, options = {})
  req = build_request(:list_reference_import_jobs, params)
  req.send_request(options)
end

#list_reference_stores(params = {}) ⇒ Types::ListReferenceStoresResponse

Retrieves a list of reference stores.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_reference_stores({
  max_results: 1,
  next_token: "NextToken",
  filter: {
    name: "ReferenceStoreName",
    created_after: Time.now,
    created_before: Time.now,
  },
})

Response structure


resp.next_token #=> String
resp.reference_stores #=> Array
resp.reference_stores[0].arn #=> String
resp.reference_stores[0].id #=> String
resp.reference_stores[0].name #=> String
resp.reference_stores[0].description #=> String
resp.reference_stores[0].sse_config.type #=> String, one of "KMS"
resp.reference_stores[0].sse_config.key_arn #=> String
resp.reference_stores[0].creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ReferenceStoreFilter) —

    A filter to apply to the list.

Returns:

See Also:



4266
4267
4268
4269
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4266

def list_reference_stores(params = {}, options = {})
  req = build_request(:list_reference_stores, params)
  req.send_request(options)
end

#list_references(params = {}) ⇒ Types::ListReferencesResponse

Retrieves a list of references.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_references({
  reference_store_id: "ReferenceStoreId", # required
  max_results: 1,
  next_token: "NextToken",
  filter: {
    name: "ReferenceName",
    md5: "Md5",
    created_after: Time.now,
    created_before: Time.now,
  },
})

Response structure


resp.next_token #=> String
resp.references #=> Array
resp.references[0].id #=> String
resp.references[0].arn #=> String
resp.references[0].reference_store_id #=> String
resp.references[0].md5 #=> String
resp.references[0].status #=> String, one of "ACTIVE", "DELETING", "DELETED"
resp.references[0].name #=> String
resp.references[0].description #=> String
resp.references[0].creation_time #=> Time
resp.references[0].update_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :reference_store_id (required, String) —

    The references' reference store ID.

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ReferenceFilter) —

    A filter to apply to the list.

Returns:

See Also:



4325
4326
4327
4328
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4325

def list_references(params = {}, options = {})
  req = build_request(:list_references, params)
  req.send_request(options)
end

#list_run_caches(params = {}) ⇒ Types::ListRunCachesResponse

Retrieves a list of your run caches and the metadata for each cache.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_run_caches({
  max_results: 1,
  starting_token: "ListToken",
})

Response structure


resp.items #=> Array
resp.items[0].arn #=> String
resp.items[0].cache_behavior #=> String, one of "CACHE_ON_FAILURE", "CACHE_ALWAYS"
resp.items[0].cache_s3_uri #=> String
resp.items[0].creation_time #=> Time
resp.items[0].id #=> String
resp.items[0].name #=> String
resp.items[0].status #=> String, one of "ACTIVE", "DELETED", "FAILED"
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

    The maximum number of results to return.

  • :starting_token (String) —

    Optional pagination token returned from a prior call to the ListRunCaches API operation.

Returns:

See Also:



4369
4370
4371
4372
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4369

def list_run_caches(params = {}, options = {})
  req = build_request(:list_run_caches, params)
  req.send_request(options)
end

#list_run_groups(params = {}) ⇒ Types::ListRunGroupsResponse

Retrieves a list of all run groups and returns the metadata for each run group.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_run_groups({
  name: "RunGroupName",
  starting_token: "RunGroupListToken",
  max_results: 1,
})

Response structure


resp.items #=> Array
resp.items[0].arn #=> String
resp.items[0].id #=> String
resp.items[0].name #=> String
resp.items[0].max_cpus #=> Integer
resp.items[0].max_runs #=> Integer
resp.items[0].max_duration #=> Integer
resp.items[0].creation_time #=> Time
resp.items[0].max_gpus #=> Integer
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (String) —

    The run groups' name.

  • :starting_token (String) —

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

  • :max_results (Integer) —

    The maximum number of run groups to return in one page of results.

Returns:

See Also:



4419
4420
4421
4422
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4419

def list_run_groups(params = {}, options = {})
  req = build_request(:list_run_groups, params)
  req.send_request(options)
end

#list_run_tasks(params = {}) ⇒ Types::ListRunTasksResponse

Returns a list of tasks and status information within their specified run. Use this operation to monitor runs and to identify which specific tasks have failed.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_run_tasks({
  id: "RunId", # required
  status: "PENDING", # accepts PENDING, STARTING, RUNNING, STOPPING, COMPLETED, CANCELLED, FAILED
  starting_token: "TaskListToken",
  max_results: 1,
})

Response structure


resp.items #=> Array
resp.items[0].task_id #=> String
resp.items[0].status #=> String, one of "PENDING", "STARTING", "RUNNING", "STOPPING", "COMPLETED", "CANCELLED", "FAILED"
resp.items[0].name #=> String
resp.items[0].cpus #=> Integer
resp.items[0].cache_hit #=> Boolean
resp.items[0].cache_s3_uri #=> String
resp.items[0].memory #=> Integer
resp.items[0].creation_time #=> Time
resp.items[0].start_time #=> Time
resp.items[0].stop_time #=> Time
resp.items[0].gpus #=> Integer
resp.items[0].instance_type #=> String
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The run's ID.

  • :status (String) —

    Filter the list by status.

  • :starting_token (String) —

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

  • :max_results (Integer) —

    The maximum number of run tasks to return in one page of results.

Returns:

See Also:



4478
4479
4480
4481
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4478

def list_run_tasks(params = {}, options = {})
  req = build_request(:list_run_tasks, params)
  req.send_request(options)
end

#list_runs(params = {}) ⇒ Types::ListRunsResponse

Retrieves a list of runs and returns each run's metadata and status.

Amazon Web Services HealthOmics stores a configurable number of runs, as determined by service limits, that are available to the console and API. If the ListRuns response doesn't include specific runs that you expected, you can find all run logs in the CloudWatch logs. For more information about viewing the run logs, see CloudWatch logs in the Amazon Web Services HealthOmics User Guide.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_runs({
  name: "RunName",
  run_group_id: "RunGroupId",
  starting_token: "RunListToken",
  max_results: 1,
  status: "PENDING", # accepts PENDING, STARTING, RUNNING, STOPPING, COMPLETED, DELETED, CANCELLED, FAILED
})

Response structure


resp.items #=> Array
resp.items[0].arn #=> String
resp.items[0].id #=> String
resp.items[0].status #=> String, one of "PENDING", "STARTING", "RUNNING", "STOPPING", "COMPLETED", "DELETED", "CANCELLED", "FAILED"
resp.items[0].workflow_id #=> String
resp.items[0].name #=> String
resp.items[0].priority #=> Integer
resp.items[0].storage_capacity #=> Integer
resp.items[0].creation_time #=> Time
resp.items[0].start_time #=> Time
resp.items[0].stop_time #=> Time
resp.items[0].storage_type #=> String, one of "STATIC", "DYNAMIC"
resp.items[0].workflow_version_name #=> String
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (String) —

    Filter the list by run name.

  • :run_group_id (String) —

    Filter the list by run group ID.

  • :starting_token (String) —

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

  • :max_results (Integer) —

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

  • :status (String) —

    The status of a run.

Returns:

See Also:



4550
4551
4552
4553
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4550

def list_runs(params = {}, options = {})
  req = build_request(:list_runs, params)
  req.send_request(options)
end

#list_sequence_stores(params = {}) ⇒ Types::ListSequenceStoresResponse

Retrieves a list of sequence stores.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_sequence_stores({
  max_results: 1,
  next_token: "NextToken",
  filter: {
    name: "SequenceStoreName",
    created_after: Time.now,
    created_before: Time.now,
    status: "CREATING", # accepts CREATING, ACTIVE, UPDATING, DELETING, FAILED
    updated_after: Time.now,
    updated_before: Time.now,
  },
})

Response structure


resp.next_token #=> String
resp.sequence_stores #=> Array
resp.sequence_stores[0].arn #=> String
resp.sequence_stores[0].id #=> String
resp.sequence_stores[0].name #=> String
resp.sequence_stores[0].description #=> String
resp.sequence_stores[0].sse_config.type #=> String, one of "KMS"
resp.sequence_stores[0].sse_config.key_arn #=> String
resp.sequence_stores[0].creation_time #=> Time
resp.sequence_stores[0].fallback_location #=> String
resp.sequence_stores[0].e_tag_algorithm_family #=> String, one of "MD5up", "SHA256up", "SHA512up"
resp.sequence_stores[0].status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETING", "FAILED"
resp.sequence_stores[0].status_message #=> String
resp.sequence_stores[0].update_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::SequenceStoreFilter) —

    A filter to apply to the list.

Returns:

See Also:



4610
4611
4612
4613
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4610

def list_sequence_stores(params = {}, options = {})
  req = build_request(:list_sequence_stores, params)
  req.send_request(options)
end

#list_shares(params = {}) ⇒ Types::ListSharesResponse

Retrieves the resource shares associated with an account. Use the filter parameter to retrieve a specific subset of the shares.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_shares({
  resource_owner: "SELF", # required, accepts SELF, OTHER
  filter: {
    resource_arns: ["String"],
    status: ["PENDING"], # accepts PENDING, ACTIVATING, ACTIVE, DELETING, DELETED, FAILED
    type: ["VARIANT_STORE"], # accepts VARIANT_STORE, ANNOTATION_STORE, WORKFLOW
  },
  next_token: "String",
  max_results: 1,
})

Response structure


resp.shares #=> Array
resp.shares[0].share_id #=> String
resp.shares[0].resource_arn #=> String
resp.shares[0].resource_id #=> String
resp.shares[0].principal_subscriber #=> String
resp.shares[0].owner_id #=> String
resp.shares[0].status #=> String, one of "PENDING", "ACTIVATING", "ACTIVE", "DELETING", "DELETED", "FAILED"
resp.shares[0].status_message #=> String
resp.shares[0].share_name #=> String
resp.shares[0].creation_time #=> Time
resp.shares[0].update_time #=> Time
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :resource_owner (required, String) —

    The account that owns the resource shares.

  • :filter (Types::Filter) —

    Attributes that you use to filter for a specific subset of resource shares.

  • :next_token (String) —

    Next token returned in the response of a previous ListReadSetUploadPartsRequest call. Used to get the next page of results.

  • :max_results (Integer) —

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

Returns:

See Also:



4672
4673
4674
4675
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4672

def list_shares(params = {}, options = {})
  req = build_request(:list_shares, params)
  req.send_request(options)
end

#list_tags_for_resource(params = {}) ⇒ Types::ListTagsForResourceResponse

Retrieves a list of tags for a resource.

Examples:

Request syntax with placeholder values


resp = client.list_tags_for_resource({
  resource_arn: "TagArn", # required
})

Response structure


resp.tags #=> Hash
resp.tags["TagKey"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :resource_arn (required, String) —

    The resource's ARN.

Returns:

See Also:



4701
4702
4703
4704
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4701

def list_tags_for_resource(params = {}, options = {})
  req = build_request(:list_tags_for_resource, params)
  req.send_request(options)
end

#list_variant_import_jobs(params = {}) ⇒ Types::ListVariantImportJobsResponse

Retrieves a list of variant import jobs.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_variant_import_jobs({
  max_results: 1,
  ids: ["ResourceIdentifier"],
  next_token: "ListVariantImportJobsRequestNextTokenString",
  filter: {
    status: "SUBMITTED", # accepts SUBMITTED, IN_PROGRESS, CANCELLED, COMPLETED, FAILED, COMPLETED_WITH_FAILURES
    store_name: "String",
  },
})

Response structure


resp.variant_import_jobs #=> Array
resp.variant_import_jobs[0].id #=> String
resp.variant_import_jobs[0].destination_name #=> String
resp.variant_import_jobs[0].role_arn #=> String
resp.variant_import_jobs[0].status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLED", "COMPLETED", "FAILED", "COMPLETED_WITH_FAILURES"
resp.variant_import_jobs[0].creation_time #=> Time
resp.variant_import_jobs[0].update_time #=> Time
resp.variant_import_jobs[0].completion_time #=> Time
resp.variant_import_jobs[0].run_left_normalization #=> Boolean
resp.variant_import_jobs[0].annotation_fields #=> Hash
resp.variant_import_jobs[0].annotation_fields["AnnotationFieldMapKeyString"] #=> String
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

    The maximum number of import jobs to return in one page of results.

  • :ids (Array<String>) —

    A list of job IDs.

  • :next_token (String) —

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

  • :filter (Types::ListVariantImportJobsFilter) —

    A filter to apply to the list.

Returns:

See Also:



4759
4760
4761
4762
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4759

def list_variant_import_jobs(params = {}, options = {})
  req = build_request(:list_variant_import_jobs, params)
  req.send_request(options)
end

#list_variant_stores(params = {}) ⇒ Types::ListVariantStoresResponse

Retrieves a list of variant stores.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_variant_stores({
  max_results: 1,
  ids: ["ResourceIdentifier"],
  next_token: "ListVariantStoresRequestNextTokenString",
  filter: {
    status: "CREATING", # accepts CREATING, UPDATING, DELETING, ACTIVE, FAILED
  },
})

Response structure


resp.variant_stores #=> Array
resp.variant_stores[0].id #=> String
resp.variant_stores[0].reference.reference_arn #=> String
resp.variant_stores[0].status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.variant_stores[0].store_arn #=> String
resp.variant_stores[0].name #=> String
resp.variant_stores[0].description #=> String
resp.variant_stores[0].sse_config.type #=> String, one of "KMS"
resp.variant_stores[0].sse_config.key_arn #=> String
resp.variant_stores[0].creation_time #=> Time
resp.variant_stores[0].update_time #=> Time
resp.variant_stores[0].status_message #=> String
resp.variant_stores[0].store_size_bytes #=> Integer
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :ids (Array<String>) —

    A list of store IDs.

  • :next_token (String) —

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

  • :filter (Types::ListVariantStoresFilter) —

    A filter to apply to the list.

Returns:

See Also:



4818
4819
4820
4821
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4818

def list_variant_stores(params = {}, options = {})
  req = build_request(:list_variant_stores, params)
  req.send_request(options)
end

#list_workflow_versions(params = {}) ⇒ Types::ListWorkflowVersionsResponse

Lists the workflow versions for the specified workflow. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_workflow_versions({
  workflow_id: "WorkflowId", # required
  type: "PRIVATE", # accepts PRIVATE, READY2RUN
  workflow_owner_id: "WorkflowOwnerId",
  starting_token: "WorkflowVersionListToken",
  max_results: 1,
})

Response structure


resp.items #=> Array
resp.items[0].arn #=> String
resp.items[0].workflow_id #=> String
resp.items[0].version_name #=> String
resp.items[0].description #=> String
resp.items[0].status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETED", "FAILED", "INACTIVE"
resp.items[0].type #=> String, one of "PRIVATE", "READY2RUN"
resp.items[0].digest #=> String
resp.items[0].creation_time #=> Time
resp.items[0].metadata #=> Hash
resp.items[0].metadata["WorkflowMetadataKey"] #=> String
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :workflow_id (required, String) —

    The workflow's ID.

  • :type (String) —

    The workflow type.

  • :workflow_owner_id (String) —

    Amazon Web Services Id of the owner of the workflow.

  • :starting_token (String) —

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

  • :max_results (Integer) —

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

Returns:

See Also:



4883
4884
4885
4886
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4883

def list_workflow_versions(params = {}, options = {})
  req = build_request(:list_workflow_versions, params)
  req.send_request(options)
end

#list_workflows(params = {}) ⇒ Types::ListWorkflowsResponse

Retrieves a list of existing workflows. You can filter for specific workflows by their name and type. Using the type parameter, specify PRIVATE to retrieve a list of private workflows or specify READY2RUN for a list of all Ready2Run workflows. If you do not specify the type of workflow, this operation returns a list of existing workflows.

The returned response is a pageable response and is Enumerable. For details on usage see PageableResponse.

Examples:

Request syntax with placeholder values


resp = client.list_workflows({
  type: "PRIVATE", # accepts PRIVATE, READY2RUN
  name: "WorkflowName",
  starting_token: "WorkflowListToken",
  max_results: 1,
})

Response structure


resp.items #=> Array
resp.items[0].arn #=> String
resp.items[0].id #=> String
resp.items[0].name #=> String
resp.items[0].status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETED", "FAILED", "INACTIVE"
resp.items[0].type #=> String, one of "PRIVATE", "READY2RUN"
resp.items[0].digest #=> String
resp.items[0].creation_time #=> Time
resp.items[0].metadata #=> Hash
resp.items[0].metadata["WorkflowMetadataKey"] #=> String
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :type (String) —

    Filter the list by workflow type.

  • :name (String) —

    Filter the list by workflow name.

  • :starting_token (String) —

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

  • :max_results (Integer) —

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

Returns:

See Also:



4942
4943
4944
4945
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4942

def list_workflows(params = {}, options = {})
  req = build_request(:list_workflows, params)
  req.send_request(options)
end

#put_s3_access_policy(params = {}) ⇒ Types::PutS3AccessPolicyResponse

Adds an access policy to the specified store.

Examples:

Request syntax with placeholder values


resp = client.put_s3_access_policy({
  s3_access_point_arn: "S3AccessPointArn", # required
  s3_access_policy: "S3AccessPolicy", # required
})

Response structure


resp.s3_access_point_arn #=> String
resp.store_id #=> String
resp.store_type #=> String, one of "SEQUENCE_STORE", "REFERENCE_STORE"

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :s3_access_point_arn (required, String) —

    The S3 access point ARN where you want to put the access policy.

  • :s3_access_policy (required, String) —

    The resource policy that controls S3 access to the store.

    SDK automatically handles json encoding and base64 encoding for you when the required value (Hash, Array, etc.) is provided according to the description.

Returns:

See Also:



4982
4983
4984
4985
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4982

def put_s3_access_policy(params = {}, options = {})
  req = build_request(:put_s3_access_policy, params)
  req.send_request(options)
end

#start_annotation_import_job(params = {}) ⇒ Types::StartAnnotationImportResponse

Starts an annotation import job.

Examples:

Request syntax with placeholder values


resp = client.start_annotation_import_job({
  destination_name: "StoreName", # required
  role_arn: "Arn", # required
  items: [ # required
    {
      source: "S3Uri", # required
    },
  ],
  version_name: "VersionName",
  format_options: {
    tsv_options: {
      read_options: {
        sep: "Separator",
        encoding: "Encoding",
        quote: "Quote",
        quote_all: false,
        escape: "EscapeChar",
        escape_quotes: false,
        comment: "CommentChar",
        header: false,
        line_sep: "LineSep",
      },
    },
    vcf_options: {
      ignore_qual_field: false,
      ignore_filter_field: false,
    },
  },
  run_left_normalization: false,
  annotation_fields: {
    "AnnotationFieldMapKeyString" => "AnnotationFieldMapValueString",
  },
})

Response structure


resp.job_id #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :destination_name (required, String) —

    A destination annotation store for the job.

  • :role_arn (required, String) —

    A service role for the job.

  • :items (required, Array<Types::AnnotationImportItemSource>) —

    Items to import.

  • :version_name (String) —

    The name of the annotation store version.

  • :format_options (Types::FormatOptions) —

    Formatting options for the annotation file.

  • :run_left_normalization (Boolean) —

    The job's left normalization setting.

  • :annotation_fields (Hash<String,String>) —

    The annotation schema generated by the parsed annotation data.

Returns:

See Also:



5058
5059
5060
5061
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5058

def start_annotation_import_job(params = {}, options = {})
  req = build_request(:start_annotation_import_job, params)
  req.send_request(options)
end

#start_read_set_activation_job(params = {}) ⇒ Types::StartReadSetActivationJobResponse

Activates an archived read set. To reduce storage charges, Amazon Omics archives unused read sets after 30 days.

Examples:

Request syntax with placeholder values


resp = client.start_read_set_activation_job({
  sequence_store_id: "SequenceStoreId", # required
  client_token: "ClientToken",
  sources: [ # required
    {
      read_set_id: "ReadSetId", # required
    },
  ],
})

Response structure


resp.id #=> String
resp.sequence_store_id #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :client_token (String) —

    To ensure that jobs don't run multiple times, specify a unique token for each job.

  • :sources (required, Array<Types::StartReadSetActivationJobSourceItem>) —

    The job's source files.

Returns:

See Also:



5106
5107
5108
5109
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5106

def start_read_set_activation_job(params = {}, options = {})
  req = build_request(:start_read_set_activation_job, params)
  req.send_request(options)
end

#start_read_set_export_job(params = {}) ⇒ Types::StartReadSetExportJobResponse

Exports a read set to Amazon S3.

Examples:

Request syntax with placeholder values


resp = client.start_read_set_export_job({
  sequence_store_id: "SequenceStoreId", # required
  destination: "S3Destination", # required
  role_arn: "RoleArn", # required
  client_token: "ClientToken",
  sources: [ # required
    {
      read_set_id: "ReadSetId", # required
    },
  ],
})

Response structure


resp.id #=> String
resp.sequence_store_id #=> String
resp.destination #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :destination (required, String) —

    A location for exported files in Amazon S3.

  • :role_arn (required, String) —

    A service role for the job.

  • :client_token (String) —

    To ensure that jobs don't run multiple times, specify a unique token for each job.

  • :sources (required, Array<Types::ExportReadSet>) —

    The job's source files.

Returns:

See Also:



5163
5164
5165
5166
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5163

def start_read_set_export_job(params = {}, options = {})
  req = build_request(:start_read_set_export_job, params)
  req.send_request(options)
end

#start_read_set_import_job(params = {}) ⇒ Types::StartReadSetImportJobResponse

Starts a read set import job.

Examples:

Request syntax with placeholder values


resp = client.start_read_set_import_job({
  sequence_store_id: "SequenceStoreId", # required
  role_arn: "RoleArn", # required
  client_token: "ClientToken",
  sources: [ # required
    {
      source_files: { # required
        source1: "S3Uri", # required
        source2: "S3Uri",
      },
      source_file_type: "FASTQ", # required, accepts FASTQ, BAM, CRAM, UBAM
      subject_id: "SubjectId", # required
      sample_id: "SampleId", # required
      generated_from: "GeneratedFrom",
      reference_arn: "ReferenceArn",
      name: "ReadSetName",
      description: "ReadSetDescription",
      tags: {
        "TagKey" => "TagValue",
      },
    },
  ],
})

Response structure


resp.id #=> String
resp.sequence_store_id #=> String
resp.role_arn #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :role_arn (required, String) —

    A service role for the job.

  • :client_token (String) —

    To ensure that jobs don't run multiple times, specify a unique token for each job.

  • :sources (required, Array<Types::StartReadSetImportJobSourceItem>) —

    The job's source files.

Returns:

See Also:



5229
5230
5231
5232
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5229

def start_read_set_import_job(params = {}, options = {})
  req = build_request(:start_read_set_import_job, params)
  req.send_request(options)
end

#start_reference_import_job(params = {}) ⇒ Types::StartReferenceImportJobResponse

Starts a reference import job.

Examples:

Request syntax with placeholder values


resp = client.start_reference_import_job({
  reference_store_id: "ReferenceStoreId", # required
  role_arn: "RoleArn", # required
  client_token: "ClientToken",
  sources: [ # required
    {
      source_file: "S3Uri", # required
      name: "ReferenceName", # required
      description: "ReferenceDescription",
      tags: {
        "TagKey" => "TagValue",
      },
    },
  ],
})

Response structure


resp.id #=> String
resp.reference_store_id #=> String
resp.role_arn #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.creation_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :reference_store_id (required, String) —

    The job's reference store ID.

  • :role_arn (required, String) —

    A service role for the job.

  • :client_token (String) —

    To ensure that jobs don't run multiple times, specify a unique token for each job.

  • :sources (required, Array<Types::StartReferenceImportJobSourceItem>) —

    The job's source files.

Returns:

See Also:



5287
5288
5289
5290
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5287

def start_reference_import_job(params = {}, options = {})
  req = build_request(:start_reference_import_job, params)
  req.send_request(options)
end

#start_run(params = {}) ⇒ Types::StartRunResponse

Starts a new run and returns details about the run, or duplicates an existing run. A run is a single invocation of a workflow. If you provide request IDs, Amazon Web Services HealthOmics identifies duplicate requests and starts the run only once. Monitor the progress of the run by calling the GetRun API operation.

To start a new run, the following inputs are required:

  • A service role ARN (roleArn).

  • The run's workflow ID (workflowId, not the uuid or runId).

  • An Amazon S3 location (outputUri) where the run outputs will be saved.

  • All required workflow parameters (parameter), which can include optional parameters from the parameter template. The run cannot include any parameters that are not defined in the parameter template. To see all possible parameters, use the GetRun API operation.

  • For runs with a STATIC (default) storage type, specify the required storage capacity (in gibibytes). A storage capacity value is not required for runs that use DYNAMIC storage.

StartRun can also duplicate an existing run using the run's default values. You can modify these default values and/or add other optional inputs. To duplicate a run, the following inputs are required:

  • A service role ARN (roleArn).

  • The ID of the run to duplicate (runId).

  • An Amazon S3 location where the run outputs will be saved (outputUri).

To learn more about the optional parameters for StartRun, see Starting a run in the Amazon Web Services HealthOmics User Guide.

Use the retentionMode input to control how long the metadata for each run is stored in CloudWatch. There are two retention modes:

  • Specify REMOVE to automatically remove the oldest runs when you reach the maximum service retention limit for runs. It is recommended that you use the REMOVE mode to initiate major run requests so that your runs do not fail when you reach the limit.

  • The retentionMode is set to the RETAIN mode by default, which allows you to manually remove runs after reaching the maximum service retention limit. Under this setting, you cannot create additional runs until you remove the excess runs.

To learn more about the retention modes, see Run retention mode in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.start_run({
  workflow_id: "WorkflowId",
  workflow_type: "PRIVATE", # accepts PRIVATE, READY2RUN
  run_id: "RunId",
  role_arn: "RunRoleArn", # required
  name: "RunName",
  cache_id: "NumericIdInArn",
  cache_behavior: "CACHE_ON_FAILURE", # accepts CACHE_ON_FAILURE, CACHE_ALWAYS
  run_group_id: "RunGroupId",
  priority: 1,
  parameters: {
  },
  storage_capacity: 1,
  output_uri: "RunOutputUri",
  log_level: "OFF", # accepts OFF, FATAL, ERROR, ALL
  tags: {
    "TagKey" => "TagValue",
  },
  request_id: "RunRequestId", # required
  retention_mode: "RETAIN", # accepts RETAIN, REMOVE
  storage_type: "STATIC", # accepts STATIC, DYNAMIC
  workflow_owner_id: "WorkflowOwnerId",
  workflow_version_name: "WorkflowVersionName",
})

Response structure


resp.arn #=> String
resp.id #=> String
resp.status #=> String, one of "PENDING", "STARTING", "RUNNING", "STOPPING", "COMPLETED", "DELETED", "CANCELLED", "FAILED"
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.uuid #=> String
resp.run_output_uri #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :workflow_id (String) —

    The run's workflow ID. The workflowId is not the UUID.

  • :workflow_type (String) —

    The run's workflow type. The workflowType must be specified if you are running a READY2RUN workflow. If you are running a PRIVATE workflow (default), you do not need to include the workflow type.

  • :run_id (String) —

    The ID of a run to duplicate.

  • :role_arn (required, String) —

    A service role for the run. The roleArn requires access to Amazon Web Services HealthOmics, S3, Cloudwatch logs, and EC2. An example roleArn is arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ. In this example, the AWS account ID is 123456789012 and the role name is omics-service-role-serviceRole-W8O1XMPL7QZ.

  • :name (String) —

    A name for the run. This is recommended to view and organize runs in the Amazon Web Services HealthOmics console and CloudWatch logs.

  • :cache_id (String) —

    Identifier of the cache associated with this run. If you don't specify a cache ID, no task outputs are cached for this run.

  • :cache_behavior (String) —

    The cache behavior for the run. You specify this value if you want to override the default behavior for the cache. You had set the default value when you created the cache. For more information, see Run cache behavior in the Amazon Web Services HealthOmics User Guide.

  • :run_group_id (String) —

    The run's group ID. Use a run group to cap the compute resources (and number of concurrent runs) for the runs that you add to the run group.

  • :priority (Integer) —

    Use the run priority (highest: 1) to establish the order of runs in a run group when you start a run. If multiple runs share the same priority, the run that was initiated first will have the higher priority. Runs that do not belong to a run group can be assigned a priority. The priorities of these runs are ranked among other runs that are not in a run group. For more information, see Run priority in the Amazon Web Services HealthOmics User Guide.

  • :parameters (Hash, Array, String, Numeric, Boolean) —

    Parameters for the run. The run needs all required parameters and can include optional parameters. The run cannot include any parameters that are not defined in the parameter template. To retrieve parameters from the run, use the GetRun API operation.

    Document type used to carry open content (Hash,Array,String,Numeric,Boolean). A document type value is serialized using the same format as its surroundings and requires no additional encoding or escaping.

  • :storage_capacity (Integer) —

    The STATIC storage capacity (in gibibytes, GiB) for this run. The default run storage capacity is 1200 GiB. If your requested storage capacity is unavailable, the system rounds up the value to the nearest 1200 GiB multiple. If the requested storage capacity is still unavailable, the system rounds up the value to the nearest 2400 GiB multiple. This field is not required if the storage type is DYNAMIC (the system ignores any value that you enter).

  • :output_uri (String) —

    An output S3 URI for the run. The S3 bucket must be in the same region as the workflow. The role ARN must have permission to write to this S3 bucket.

  • :log_level (String) —

    A log level for the run.

  • :tags (Hash<String,String>) —

    Tags for the run. You can add up to 50 tags per run. For more information, see Adding a tag in the Amazon Web Services HealthOmics User Guide.

  • :request_id (required, String) —

    An idempotency token used to dedupe retry requests so that duplicate runs are not created.

    A suitable default value is auto-generated. You should normally not need to pass this option.**

  • :retention_mode (String) —

    The retention mode for the run. The default value is RETAIN.

    Amazon Web Services HealthOmics stores a fixed number of runs that are available to the console and API. In the default mode (RETAIN), you need to remove runs manually when the number of run exceeds the maximum. If you set the retention mode to REMOVE, Amazon Web Services HealthOmics automatically removes runs (that have mode set to REMOVE) when the number of run exceeds the maximum. All run logs are available in CloudWatch logs, if you need information about a run that is no longer available to the API.

    For more information about retention mode, see Specifying run retention mode in the Amazon Web Services HealthOmics User Guide.

  • :storage_type (String) —

    The storage type for the run. If you set the storage type to DYNAMIC, Amazon Web Services HealthOmics dynamically scales the storage up or down, based on file system utilization. By default, the run uses STATIC storage type, which allocates a fixed amount of storage. For more information about DYNAMIC and STATIC storage, see Run storage types in the Amazon Web Services HealthOmics User Guide.

  • :workflow_owner_id (String) —

    The 12-digit account ID of the workflow owner that is used for running a shared workflow. The workflow owner ID can be retrieved using the GetShare API operation. If you are the workflow owner, you do not need to include this ID.

  • :workflow_version_name (String) —

    The name of the workflow version. Use workflow versions to track and organize changes to the workflow. If your workflow has multiple versions, the run uses the default version unless you specify a version name. To learn more, see Workflow versioning in the Amazon Web Services HealthOmics User Guide.

Returns:

See Also:



5551
5552
5553
5554
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5551

def start_run(params = {}, options = {})
  req = build_request(:start_run, params)
  req.send_request(options)
end

#start_variant_import_job(params = {}) ⇒ Types::StartVariantImportResponse

Starts a variant import job.

Examples:

Request syntax with placeholder values


resp = client.start_variant_import_job({
  destination_name: "StoreName", # required
  role_arn: "Arn", # required
  items: [ # required
    {
      source: "S3Uri", # required
    },
  ],
  run_left_normalization: false,
  annotation_fields: {
    "AnnotationFieldMapKeyString" => "AnnotationFieldMapValueString",
  },
})

Response structure


resp.job_id #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :destination_name (required, String) —

    The destination variant store for the job.

  • :role_arn (required, String) —

    A service role for the job.

  • :items (required, Array<Types::VariantImportItemSource>) —

    Items to import.

  • :run_left_normalization (Boolean) —

    The job's left normalization setting.

  • :annotation_fields (Hash<String,String>) —

    The annotation schema generated by the parsed annotation data.

Returns:

See Also:



5601
5602
5603
5604
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5601

def start_variant_import_job(params = {}, options = {})
  req = build_request(:start_variant_import_job, params)
  req.send_request(options)
end

#tag_resource(params = {}) ⇒ Struct

Tags a resource.

Examples:

Request syntax with placeholder values


resp = client.tag_resource({
  resource_arn: "TagArn", # required
  tags: { # required
    "TagKey" => "TagValue",
  },
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :resource_arn (required, String) —

    The resource's ARN.

  • :tags (required, Hash<String,String>) —

    Tags for the resource.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



5629
5630
5631
5632
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5629

def tag_resource(params = {}, options = {})
  req = build_request(:tag_resource, params)
  req.send_request(options)
end

#untag_resource(params = {}) ⇒ Struct

Removes tags from a resource.

Examples:

Request syntax with placeholder values


resp = client.untag_resource({
  resource_arn: "TagArn", # required
  tag_keys: ["TagKey"], # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :resource_arn (required, String) —

    The resource's ARN.

  • :tag_keys (required, Array<String>) —

    Keys of tags to remove.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



5655
5656
5657
5658
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5655

def untag_resource(params = {}, options = {})
  req = build_request(:untag_resource, params)
  req.send_request(options)
end

#update_annotation_store(params = {}) ⇒ Types::UpdateAnnotationStoreResponse

Updates an annotation store.

Examples:

Request syntax with placeholder values


resp = client.update_annotation_store({
  name: "String", # required
  description: "Description",
})

Response structure


resp.id #=> String
resp.reference.reference_arn #=> String
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.name #=> String
resp.description #=> String
resp.creation_time #=> Time
resp.update_time #=> Time
resp.store_options.tsv_store_options.annotation_type #=> String, one of "GENERIC", "CHR_POS", "CHR_POS_REF_ALT", "CHR_START_END_ONE_BASE", "CHR_START_END_REF_ALT_ONE_BASE", "CHR_START_END_ZERO_BASE", "CHR_START_END_REF_ALT_ZERO_BASE"
resp.store_options.tsv_store_options.format_to_header #=> Hash
resp.store_options.tsv_store_options.format_to_header["FormatToHeaderKey"] #=> String
resp.store_options.tsv_store_options.schema #=> Array
resp.store_options.tsv_store_options.schema[0] #=> Hash
resp.store_options.tsv_store_options.schema[0]["SchemaItemKeyString"] #=> String, one of "LONG", "INT", "STRING", "FLOAT", "DOUBLE", "BOOLEAN"
resp.store_format #=> String, one of "GFF", "TSV", "VCF"

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    A name for the store.

  • :description (String) —

    A description for the store.

Returns:

See Also:



5708
5709
5710
5711
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5708

def update_annotation_store(params = {}, options = {})
  req = build_request(:update_annotation_store, params)
  req.send_request(options)
end

#update_annotation_store_version(params = {}) ⇒ Types::UpdateAnnotationStoreVersionResponse

Updates the description of an annotation store version.

Examples:

Request syntax with placeholder values


resp = client.update_annotation_store_version({
  name: "String", # required
  version_name: "String", # required
  description: "Description",
})

Response structure


resp.store_id #=> String
resp.id #=> String
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.name #=> String
resp.version_name #=> String
resp.description #=> String
resp.creation_time #=> Time
resp.update_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The name of an annotation store.

  • :version_name (required, String) —

    The name of an annotation store version.

  • :description (String) —

    The description of an annotation store.

Returns:

See Also:



5758
5759
5760
5761
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5758

def update_annotation_store_version(params = {}, options = {})
  req = build_request(:update_annotation_store_version, params)
  req.send_request(options)
end

#update_run_cache(params = {}) ⇒ Struct

Updates a run cache using its ID and returns a response with no body if the operation is successful. You can update the run cache description, name, or the default run cache behavior with CACHE_ON_FAILURE or CACHE_ALWAYS. To confirm that your run cache settings have been properly updated, use the GetRunCache API operation.

For more information, see How call caching works in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.update_run_cache({
  cache_behavior: "CACHE_ON_FAILURE", # accepts CACHE_ON_FAILURE, CACHE_ALWAYS
  description: "UserCustomDescription",
  id: "RunCacheId", # required
  name: "UserCustomName",
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :cache_behavior (String) —

    Update the default run cache behavior.

  • :description (String) —

    Update the run cache description.

  • :id (required, String) —

    The identifier of the run cache you want to update.

  • :name (String) —

    Update the name of the run cache.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



5804
5805
5806
5807
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5804

def update_run_cache(params = {}, options = {})
  req = build_request(:update_run_cache, params)
  req.send_request(options)
end

#update_run_group(params = {}) ⇒ Struct

Updates the settings of a run group and returns a response with no body if the operation is successful.

You can update the following settings with UpdateRunGroup:

  • Maximum number of CPUs

  • Run time (measured in minutes)

  • Number of GPUs

  • Number of concurrent runs

  • Group name

To confirm that the settings have been successfully updated, use the ListRunGroups or GetRunGroup API operations to verify that the desired changes have been made.

Examples:

Request syntax with placeholder values


resp = client.update_run_group({
  id: "RunGroupId", # required
  name: "RunGroupName",
  max_cpus: 1,
  max_runs: 1,
  max_duration: 1,
  max_gpus: 1,
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The group's ID.

  • :name (String) —

    A name for the group.

  • :max_cpus (Integer) —

    The maximum number of CPUs to use.

  • :max_runs (Integer) —

    The maximum number of concurrent runs for the group.

  • :max_duration (Integer) —

    A maximum run time for the group in minutes.

  • :max_gpus (Integer) —

    The maximum GPUs that can be used by a run group.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



5863
5864
5865
5866
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5863

def update_run_group(params = {}, options = {})
  req = build_request(:update_run_group, params)
  req.send_request(options)
end

#update_sequence_store(params = {}) ⇒ Types::UpdateSequenceStoreResponse

Update one or more parameters for the sequence store.

Examples:

Request syntax with placeholder values


resp = client.update_sequence_store({
  id: "SequenceStoreId", # required
  name: "SequenceStoreName",
  description: "SequenceStoreDescription",
  client_token: "ClientToken",
  fallback_location: "FallbackLocation",
  propagated_set_level_tags: ["TagKey"],
  s3_access_config: {
    access_log_location: "AccessLogLocation",
  },
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.name #=> String
resp.description #=> String
resp.sse_config.type #=> String, one of "KMS"
resp.sse_config.key_arn #=> String
resp.creation_time #=> Time
resp.update_time #=> Time
resp.propagated_set_level_tags #=> Array
resp.propagated_set_level_tags[0] #=> String
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETING", "FAILED"
resp.status_message #=> String
resp.fallback_location #=> String
resp.s3_access.s3_uri #=> String
resp.s3_access.s3_access_point_arn #=> String
resp.s3_access.access_log_location #=> String
resp.e_tag_algorithm_family #=> String, one of "MD5up", "SHA256up", "SHA512up"

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The ID of the sequence store.

  • :name (String) —

    A name for the sequence store.

  • :description (String) —

    A description for the sequence store.

  • :client_token (String) —

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

    A suitable default value is auto-generated. You should normally not need to pass this option.**

  • :fallback_location (String) —

    The S3 URI of a bucket and folder to store Read Sets that fail to upload.

  • :propagated_set_level_tags (Array<String>) —

    The tags keys to propagate to the S3 objects associated with read sets in the sequence store.

  • :s3_access_config (Types::S3AccessConfig) —

    S3 access configuration parameters.

Returns:

See Also:



5951
5952
5953
5954
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5951

def update_sequence_store(params = {}, options = {})
  req = build_request(:update_sequence_store, params)
  req.send_request(options)
end

#update_variant_store(params = {}) ⇒ Types::UpdateVariantStoreResponse

Updates a variant store.

Examples:

Request syntax with placeholder values


resp = client.update_variant_store({
  name: "String", # required
  description: "Description",
})

Response structure


resp.id #=> String
resp.reference.reference_arn #=> String
resp.status #=> String, one of "CREATING", "UPDATING", "DELETING", "ACTIVE", "FAILED"
resp.name #=> String
resp.description #=> String
resp.creation_time #=> Time
resp.update_time #=> Time

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    A name for the store.

  • :description (String) —

    A description for the store.

Returns:

See Also:



5995
5996
5997
5998
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 5995

def update_variant_store(params = {}, options = {})
  req = build_request(:update_variant_store, params)
  req.send_request(options)
end

#update_workflow(params = {}) ⇒ Struct

Updates information about a workflow.

You can update the following workflow information:

  • Name

  • Description

  • Default storage type

  • Default storage capacity (with workflow ID)

This operation returns a response with no body if the operation is successful. You can check the workflow updates by calling the GetWorkflow API operation.

For more information, see Update a private workflow in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.update_workflow({
  id: "WorkflowId", # required
  name: "WorkflowName",
  description: "WorkflowDescription",
  storage_type: "STATIC", # accepts STATIC, DYNAMIC
  storage_capacity: 1,
  readme_markdown: "ReadmeMarkdown",
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The workflow's ID.

  • :name (String) —

    A name for the workflow.

  • :description (String) —

    A description for the workflow.

  • :storage_type (String) —

    The default storage type for runs that use this workflow. STATIC storage allocates a fixed amount of storage. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. For more information about static and dynamic storage, see Running workflows in the Amazon Web Services HealthOmics User Guide.

  • :storage_capacity (Integer) —

    The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.

  • :readme_markdown (String) —

    The markdown content for the workflow's README file. This provides documentation and usage information for users of the workflow.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



6069
6070
6071
6072
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 6069

def update_workflow(params = {}, options = {})
  req = build_request(:update_workflow, params)
  req.send_request(options)
end

#update_workflow_version(params = {}) ⇒ Struct

Updates information about the workflow version. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.

Examples:

Request syntax with placeholder values


resp = client.update_workflow_version({
  workflow_id: "WorkflowId", # required
  version_name: "WorkflowVersionName", # required
  description: "WorkflowVersionDescription",
  storage_type: "STATIC", # accepts STATIC, DYNAMIC
  storage_capacity: 1,
  readme_markdown: "ReadmeMarkdown",
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :workflow_id (required, String) —

    The workflow's ID.

  • :version_name (required, String) —

    The name of the workflow version.

  • :description (String) —

    Description of the workflow version.

  • :storage_type (String) —

    The default storage type for runs that use this workflow. STATIC storage allocates a fixed amount of storage. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. For more information about static and dynamic storage, see Running workflows in the Amazon Web Services HealthOmics User Guide.

  • :storage_capacity (Integer) —

    The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.

  • :readme_markdown (String) —

    The markdown content for the workflow version's README file. This provides documentation and usage information for users of this specific workflow version.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



6129
6130
6131
6132
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 6129

def update_workflow_version(params = {}, options = {})
  req = build_request(:update_workflow_version, params)
  req.send_request(options)
end

#upload_read_set_part(params = {}) ⇒ Types::UploadReadSetPartResponse

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.

Examples:

Request syntax with placeholder values


resp = client.upload_read_set_part({
  sequence_store_id: "SequenceStoreId", # required
  upload_id: "UploadId", # required
  part_source: "SOURCE1", # required, accepts SOURCE1, SOURCE2
  part_number: 1, # required
  payload: "data", # required
})

Response structure


resp.checksum #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The Sequence Store ID used for the multipart upload.

  • :upload_id (required, String) —

    The ID for the initiated multipart upload.

  • :part_source (required, String) —

    The source file for an upload part.

  • :part_number (required, Integer) —

    The number of the part being uploaded.

  • :payload (required, String, IO) —

    The read set data to upload for a part.

Returns:

See Also:



6175
6176
6177
6178
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 6175

def upload_read_set_part(params = {}, options = {})
  req = build_request(:upload_read_set_part, params)
  req.send_request(options)
end

#wait_until(waiter_name, params = {}, options = {}) {|w.waiter| ... } ⇒ Boolean

Polls an API operation until a resource enters a desired state.

Basic Usage

A waiter will call an API operation until:

  • It is successful
  • It enters a terminal state
  • It makes the maximum number of attempts

In between attempts, the waiter will sleep.

# polls in a loop, sleeping between attempts
client.wait_until(waiter_name, params)

Configuration

You can configure the maximum number of polling attempts, and the delay (in seconds) between each polling attempt. You can pass configuration as the final arguments hash.

# poll for ~25 seconds
client.wait_until(waiter_name, params, {
  max_attempts: 5,
  delay: 5,
})

Callbacks

You can be notified before each polling attempt and before each delay. If you throw :success or :failure from these callbacks, it will terminate the waiter.

started_at = Time.now
client.wait_until(waiter_name, params, {

  # disable max attempts
  max_attempts: nil,

  # poll for 1 hour, instead of a number of attempts
  before_wait: -> (attempts, response) do
    throw :failure if Time.now - started_at > 3600
  end
})

Handling Errors

When a waiter is unsuccessful, it will raise an error. All of the failure errors extend from Waiters::Errors::WaiterFailed.

begin
  client.wait_until(...)
rescue Aws::Waiters::Errors::WaiterFailed
  # resource did not enter the desired state in time
end

Valid Waiters

The following table lists the valid waiter names, the operations they call, and the default :delay and :max_attempts values.

waiter_name params :delay :max_attempts
annotation_import_job_created #get_annotation_import_job 30 20
annotation_store_created #get_annotation_store 30 20
annotation_store_deleted #get_annotation_store 30 20
annotation_store_version_created #get_annotation_store_version 30 20
annotation_store_version_deleted #get_annotation_store_version 30 20
read_set_activation_job_completed #get_read_set_activation_job 30 20
read_set_export_job_completed #get_read_set_export_job 30 20
read_set_import_job_completed #get_read_set_import_job 30 20
reference_import_job_completed #get_reference_import_job 30 20
run_completed #get_run 30 20
run_running #get_run 30 20
task_completed #get_run_task 30 20
task_running #get_run_task 30 20
variant_import_job_created #get_variant_import_job 30 20
variant_store_created #get_variant_store 30 20
variant_store_deleted #get_variant_store 30 20
workflow_active #get_workflow 3 10
workflow_version_active #get_workflow_version 3 10

Parameters:

  • waiter_name (Symbol)
  • params (Hash) (defaults to: {}) —

    ({})

  • options (Hash) (defaults to: {}) —

    ({})

Options Hash (options):

  • :max_attempts (Integer)
  • :delay (Integer)
  • :before_attempt (Proc)
  • :before_wait (Proc)

Yields:

  • (w.waiter)

Returns:

  • (Boolean) —

    Returns true if the waiter was successful.

Raises:

  • (Errors::FailureStateError) —

    Raised when the waiter terminates because the waiter has entered a state that it will not transition out of, preventing success.

  • (Errors::TooManyAttemptsError) —

    Raised when the configured maximum number of attempts have been made, and the waiter is not yet successful.

  • (Errors::UnexpectedError) —

    Raised when an error is encounted while polling for a resource that is not expected.

  • (Errors::NoSuchWaiterError) —

    Raised when you request to wait for an unknown state.



6307
6308
6309
6310
6311
 
# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 6307

def wait_until(waiter_name, params = {}, options = {})
  w = waiter(waiter_name, options)
  yield(w.waiter) if block_given? # deprecated
  w.wait(params)
end