Class: Aws::Omics::Client

Inherits:
Seahorse::Client::Base
  • Object
show all
Includes:
ClientStubs
Defined in:
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](/sdk-for-ruby/v3/developer-guide/setup-config.html).

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

Class Attribute Summary collapse

API Operations collapse

Class Method Summary collapse

Instance Method Summary collapse

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`

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

    • ‘ENV`, `ENV`, `ENV`, and `ENV`.

    • ‘~/.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` 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:

  • :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` 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 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 the 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` - A retry mode that includes all the functionality of `standard` mode along with automatic client side throttling.

  • :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:

  • :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 ‘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.



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# File 'lib/aws-sdk-omics/client.rb', line 471

def initialize(*args)
  super
end

Class Attribute Details

.identifier ⇒ Object (readonly)

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



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# File 'lib/aws-sdk-omics/client.rb', line 7530

def identifier
  @identifier
end

Class Method Details

.errors_module ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



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# File 'lib/aws-sdk-omics/client.rb', line 7533

def errors_module
  Errors
end

Instance Method Details

#abort_multipart_read_set_upload(params = {}) ⇒ Struct

Stops a multipart read set upload into a sequence store and returns a response with no body if the operation is successful. To confirm that a multipart read set upload has been stopped, use the ‘ListMultipartReadSetUploads` API operation to view all active multipart read set uploads.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 502

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:



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# File 'lib/aws-sdk-omics/client.rb', line 530

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. If the operation is successful, it returns a response with no body. If there is an error with deleting one of the read sets, the operation returns an error list. If the operation successfully deletes only a subset of files, it will return an error list for the remaining files that fail to be deleted. There is a limit of 100 read sets that can be deleted in each ‘BatchDeleteReadSet` API call.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 571

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

#build_request(operation_name, params = {}) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Parameters:

  • params ({}) (defaults to: {}) 


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# File 'lib/aws-sdk-omics/client.rb', line 7356

def build_request(operation_name, params = {})
  handlers = @handlers.for(operation_name)
  tracer = config.telemetry_provider.tracer_provider.tracer(
    Aws::Telemetry.module_to_tracer_name('Aws::Omics')
  )
  context = Seahorse::Client::RequestContext.new(
    operation_name: operation_name,
    operation: config.api.operation(operation_name),
    client: self,
    params: params,
    config: config,
    tracer: tracer
  )
  context[:gem_name] = 'aws-sdk-omics'
  context[:gem_version] = '1.69.0'
  Seahorse::Client::Request.new(handlers, context)
end

#cancel_annotation_import_job(params = {}) ⇒ Struct

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Cancels an annotation import job.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 603

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:



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# File 'lib/aws-sdk-omics/client.rb', line 627

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

#cancel_run_batch(params = {}) ⇒ Struct

Cancels all runs within a specified batch. This operation prevents not-yet-submitted runs from starting and submits ‘CancelRun` requests for runs that have already started.

Cancel is only allowed on batches in ‘PENDING`, `SUBMITTING`, or `INPROGRESS` state. Cancel operations are non-atomic and may be partially successful. Use `GetBatch` to review `successfulCancelSubmissionCount` and `failedCancelSubmissionCount` in the `submissionSummary`. Only one cancel or delete operation per batch is allowed at a time.

Examples:

Request syntax with placeholder values


resp = client.cancel_run_batch({
  batch_id: "BatchId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :batch_id (required, String) —

    The identifier portion of the run batch ARN.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 658

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

#cancel_variant_import_job(params = {}) ⇒ Struct

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Cancels a variant import job.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 690

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

Completes a multipart read set upload into a sequence store after you have initiated the upload process with ‘CreateMultipartReadSetUpload` and uploaded all read set parts using `UploadReadSetPart`. You must specify the parts you uploaded using the parts parameter. If the operation is successful, it returns the read set ID(s) of the uploaded read set(s).

For more information, see [Direct upload to a sequence store] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/synchronous-uploads.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 744

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Creates an annotation store.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 849

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:



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# File 'lib/aws-sdk-omics/client.rb', line 926

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

#create_configuration(params = {}) ⇒ Types::CreateConfigurationResponse

Create a new configuration.

Examples:

Request syntax with placeholder values


resp = client.create_configuration({
  name: "ConfigurationName", # required
  description: "ConfigurationDescription",
  run_configurations: { # required
    vpc_config: {
      security_group_ids: ["SecurityGroupId"],
      subnet_ids: ["SubnetId"],
    },
  },
  tags: {
    "TagKey" => "TagValue",
  },
  request_id: "ConfigurationRequestId", # required
})

Response structure


resp.arn #=> String
resp.uuid #=> String
resp.name #=> String
resp.description #=> String
resp.run_configurations.vpc_config.security_group_ids #=> Array
resp.run_configurations.vpc_config.security_group_ids[0] #=> String
resp.run_configurations.vpc_config.subnet_ids #=> Array
resp.run_configurations.vpc_config.subnet_ids[0] #=> String
resp.run_configurations.vpc_config.vpc_id #=> String
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETING", "DELETED", "FAILED"
resp.creation_time #=> Time
resp.tags #=> Hash
resp.tags["TagKey"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    User-friendly name for the configuration.

  • :description (String) —

    Optional description for the configuration.

  • :run_configurations (required, Types::RunConfigurations) —

    Required run-specific configurations.

  • :tags (Hash<String,String>) —

    Optional tags for the configuration.

  • :request_id (required, String) —

    Optional request idempotency token. If not specified, a universally unique identifier (UUID) will be automatically generated for the request.

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

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 1001

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

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

Initiates a multipart read set upload for uploading partitioned source files into a sequence store. You can directly import source files from an EC2 instance and other local compute, or from an S3 bucket. To separate these source files into parts, use the ‘split` operation. Each part cannot be larger than 100 MB. If the operation is successful, it provides an `uploadId` which is required by the `UploadReadSetPart` API operation to upload parts into a sequence store.

To continue uploading a multipart read set into your sequence store, you must use the ‘UploadReadSetPart` API operation to upload each part individually following the steps below:

  • Specify the ‘uploadId` obtained from the previous call to `CreateMultipartReadSetUpload`.

  • Upload parts for that ‘uploadId`.

When you have finished uploading parts, use the ‘CompleteMultipartReadSetUpload` API to complete the multipart read set upload and to retrieve the final read set IDs in the response.

To learn more about creating parts and the ‘split` operation, see

Direct upload to a sequence store][1

in the *Amazon Web Services

HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/synchronous-uploads.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 1118

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 and returns metadata in JSON format. Reference stores are used to store reference genomes in FASTA format. A reference store is created when the first reference genome is imported. To import additional reference genomes from an Amazon S3 bucket, use the ‘StartReferenceImportJob` API operation.

For more information, see [Creating a HealthOmics reference store] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/create-reference-store.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 1190

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/workflows-call-caching.html [2]: docs.aws.amazon.com/omics/latest/dev/workflow-cache-create.html

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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/how-run-cache.html#run-cache-behavior

  • :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:



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# File 'lib/aws-sdk-omics/client.rb', line 1295

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:



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# File 'lib/aws-sdk-omics/client.rb', line 1363

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 and returns its metadata. Sequence stores are used to store sequence data files called read sets that are saved in FASTQ, BAM, uBAM, or CRAM formats. For aligned formats (BAM and CRAM), a sequence store can only use one reference genome. For unaligned formats (FASTQ and uBAM), a reference genome is not required. You can create multiple sequence stores per region per account.

The following are optional parameters you can specify for your sequence store:

  • Use ‘s3AccessConfig` to configure your sequence store with S3 access logs (recommended).

  • Use ‘sseConfig` to define your own KMS key for encryption.

  • Use ‘eTagAlgorithmFamily` to define which algorithm to use for the HealthOmics eTag on objects.

  • Use ‘fallbackLocation` to define a backup location for storing files that have failed a direct upload.

  • Use ‘propagatedSetLevelTags` to configure tags that propagate to all objects in your store.

For more information, see [Creating a HealthOmics sequence store] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/create-sequence-store.html

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. You can configure up to 50 tags.

  • :client_token (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.**

  • :fallback_location (String) —

    An S3 location that is used to store files that have failed a direct upload. You can add or change the ‘fallbackLocation` after creating a sequence store. This is not required if you are uploading files from a different S3 bucket.

  • :e_tag_algorithm_family (String) —

    The ETag algorithm family to use for ingested read sets. The default value is MD5up. For more information on ETags, see [ETags and data provenance] in the *Amazon Web Services HealthOmics User Guide*.

    [1]: docs.aws.amazon.com/omics/latest/dev/etags-and-provenance.html

  • :propagated_set_level_tags (Array<String>) —

    The tags keys to propagate to the S3 objects associated with read sets in the sequence store. These tags can be used as input to add metadata to your read sets.

  • :s3_access_config (Types::S3AccessConfig) —

    S3 access configuration parameters. This specifies the parameters needed to access logs stored in S3 buckets. The S3 bucket must be in the same region and account as the sequence store.

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 1502

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:



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# File 'lib/aws-sdk-omics/client.rb', line 1553

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

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Creates a variant store.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 1622

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 file:* A workflow definition file 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. For more information, see [Workflow definition files] in Amazon Web Services HealthOmics.

    • You can use Amazon Q CLI to build and validate your workflow definition files in WDL, Nextflow, and CWL. For more information, see [Example prompts for Amazon Q CLI] and the [Amazon Web Services HealthOmics Agentic generative AI tutorial] on GitHub.

    ^

  • *(Optional) Parameter template file:* A parameter template file written in JSON. Create the file to define the run parameters, or Amazon Web Services HealthOmics generates the parameter template for you. For more information, see [Parameter template files for HealthOmics workflows].

  • *ECR container images:* Create container images for the workflow in a private ECR repository, or synchronize images from a supported upstream registry with your Amazon ECR private repository.

  • *(Optional) Sentieon licenses:* Request a Sentieon license to use the Sentieon software in private workflows.

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

[1]: docs.aws.amazon.com/omics/latest/dev/workflow-definition-files.html [2]: docs.aws.amazon.com/omics/latest/dev/getting-started.html#omics-q-prompts [3]: github.com/aws-samples/aws-healthomics-tutorials/tree/main/generative-ai [4]: docs.aws.amazon.com/omics/latest/dev/parameter-templates.html [5]: docs.aws.amazon.com/omics/latest/dev/creating-private-workflows.html

Examples:

Request syntax with placeholder values


resp = client.create_workflow({
  name: "WorkflowName",
  description: "WorkflowDescription",
  engine: "WDL", # accepts WDL, NEXTFLOW, CWL, WDL_LENIENT
  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
  container_registry_map: {
    registry_mappings: [
      {
        upstream_registry_url: "Uri",
        ecr_repository_prefix: "EcrRepositoryPrefix",
        upstream_repository_prefix: "UpstreamRepositoryPrefix",
        ecr_account_id: "AwsAccountId",
      },
    ],
    image_mappings: [
      {
        source_image: "Uri",
        destination_image: "Uri",
      },
    ],
  },
  container_registry_map_uri: "Uri",
  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. By default, Amazon Web Services HealthOmics detects the engine automatically from your workflow definition. Provide a value if you have workflow definition files from more than one engine in your zip file, or to use WDL lenient.

    WDL lenient is designed to handle workflows migrated from Cromwell. It supports customer Cromwell directives and some non-conformant logic. For details, see [Implicit type conversion in WDL lenient] in the *Amazon Web Services HealthOmics User Guide*.

    [1]: docs.aws.amazon.com/omics/latest/dev/workflow-wdl-type-conversion.html

  • :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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/workflow-defn-requirements.html

  • :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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/parameter-templates.html

  • :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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/add-a-tag.html

  • :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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/workflows-run-types.html

  • :container_registry_map (Types::ContainerRegistryMap) — default: Optional —

    Use a container registry map to specify mappings between the ECR private repository and one or more upstream registries. For more information, see [Container images] in the *Amazon Web Services HealthOmics User Guide*.

    [1]: docs.aws.amazon.com/omics/latest/dev/workflows-ecr.html

  • :container_registry_map_uri (String) — default: Optional —

    URI of the S3 location for the registry mapping file.

  • :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:



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# File 'lib/aws-sdk-omics/client.rb', line 1888

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.

<note markdown=“1”> Don’t include any personally identifiable information (PII) in the version name. Version names appear in the workflow version ARN.

</note>

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

[1]: docs.aws.amazon.com/omics/latest/dev/workflow-versions.html

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, WDL_LENIENT
  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",
  container_registry_map: {
    registry_mappings: [
      {
        upstream_registry_url: "Uri",
        ecr_repository_prefix: "EcrRepositoryPrefix",
        upstream_repository_prefix: "UpstreamRepositoryPrefix",
        ecr_account_id: "AwsAccountId",
      },
    ],
    image_mappings: [
      {
        source_image: "Uri",
        destination_image: "Uri",
      },
    ],
  },
  container_registry_map_uri: "Uri",
  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. The ‘workflowId` is not the UUID.

  • :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 main workflow definition file and dependencies that it imports for this workflow version. 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 this workflow version. The S3 bucket must be in the same region as 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. 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.

  • :main (String) —

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

    [1]: docs.aws.amazon.com/omics/latest/dev/parameter-templates.html

  • :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.**

  • :storage_type (String) —

    The default storage type for runs that use this workflow version. 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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/workflows-run-types.html

  • :storage_capacity (Integer) —

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

    [1]: docs.aws.amazon.com/omics/latest/dev/add-a-tag.html

  • :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.

  • :container_registry_map (Types::ContainerRegistryMap) — default: Optional —

    Use a container registry map to specify mappings between the ECR private repository and one or more upstream registries. For more information, see [Container images] in the *Amazon Web Services HealthOmics User Guide*.

    [1]: docs.aws.amazon.com/omics/latest/dev/workflows-ecr.html

  • :container_registry_map_uri (String) — default: Optional —

    URI of the S3 location for the registry mapping file.

  • :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:



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# File 'lib/aws-sdk-omics/client.rb', line 2137

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

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Deletes an annotation store.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2179

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2219

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

#delete_batch(params = {}) ⇒ Struct

Deletes a run batch resource and its associated metadata. This operation does not delete the individual workflow runs. To delete the runs, call ‘DeleteRunBatch` before calling `DeleteBatch`.

‘DeleteBatch` requires the batch to be in a terminal state: `PROCESSED`, `FAILED`, `CANCELLED`, or `RUNS_DELETED`. After `DeleteBatch` completes, the batch metadata is no longer accessible. You cannot call `GetBatch`, `ListRunsInBatch`, `DeleteRunBatch`, or `CancelRunBatch` on a deleted batch.

Examples:

Request syntax with placeholder values


resp = client.delete_batch({
  batch_id: "BatchId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :batch_id (required, String) —

    The identifier portion of the run batch ARN.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 2249

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

#delete_configuration(params = {}) ⇒ Struct

Delete an existing configuration.

Examples:

Request syntax with placeholder values


resp = client.delete_configuration({
  name: "ConfigurationName", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    Configuration name to delete.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 2271

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

#delete_reference(params = {}) ⇒ Struct

Deletes a reference genome and returns a response with no body if the operation is successful. The read set associated with the reference genome must first be deleted before deleting the reference genome. After the reference genome is deleted, you can delete the reference store using the ‘DeleteReferenceStore` API operation.

For more information, see [Deleting HealthOmics reference and sequence stores] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/deleting-reference-and-sequence-stores.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2308

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

#delete_reference_store(params = {}) ⇒ Struct

Deletes a reference store and returns a response with no body if the operation is successful. You can only delete a reference store when it does not contain any reference genomes. To empty a reference store, use ‘DeleteReference`.

For more information about your workflow status, see [Deleting HealthOmics reference and sequence stores] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/deleting-reference-and-sequence-stores.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2341

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2375

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

#delete_run_batch(params = {}) ⇒ Struct

Deletes the individual workflow runs within a batch. This operation is separate from ‘DeleteBatch`, which removes the batch metadata.

Delete is only allowed on batches in ‘PROCESSED` or `CANCELLED` state. Delete operations are non-atomic and may be partially successful. Use `GetBatch` to review `successfulDeleteSubmissionCount` and `failedDeleteSubmissionCount` in the `submissionSummary`. Only one cancel or delete operation per batch is allowed at a time.

Examples:

Request syntax with placeholder values


resp = client.delete_run_batch({
  batch_id: "BatchId", # required
})

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :batch_id (required, String) —

    The identifier portion of the run batch ARN.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 2404

def delete_run_batch(params = {}, options = {})
  req = build_request(:delete_run_batch, 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*.

[1]: docs.aws.amazon.com/omics/latest/dev/workflow-cache-delete.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2438

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2468

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2490

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 and returns a response with no body if the operation is successful. You can only delete a sequence store when it does not contain any read sets.

Use the ‘BatchDeleteReadSet` API operation to ensure that all read sets in the sequence store are deleted. When a sequence store is deleted, all tags associated with the store are also deleted.

For more information, see [Deleting HealthOmics reference and sequence stores] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/deleting-reference-and-sequence-stores.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2525

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2555

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

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Deletes a variant store.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2597

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. This operation returns a response with no body 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:



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# File 'lib/aws-sdk-omics/client.rb', line 2627

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/workflow-versions.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2661

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Gets information about an annotation import job.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2741

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Gets information about an annotation store.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2820

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:



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# File 'lib/aws-sdk-omics/client.rb', line 2890

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

#get_batch(params = {}) ⇒ Types::GetBatchResponse

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

Examples:

Request syntax with placeholder values


resp = client.get_batch({
  batch_id: "BatchId", # required
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.uuid #=> String
resp.name #=> String
resp.status #=> String, one of "CREATING", "PENDING", "SUBMITTING", "INPROGRESS", "STOPPING", "CANCELLED", "FAILED", "PROCESSED", "RUNS_DELETING", "RUNS_DELETED"
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.total_runs #=> Integer
resp.default_run_setting.workflow_id #=> String
resp.default_run_setting.workflow_type #=> String, one of "PRIVATE", "READY2RUN"
resp.default_run_setting.role_arn #=> String
resp.default_run_setting.name #=> String
resp.default_run_setting.cache_id #=> String
resp.default_run_setting.cache_behavior #=> String, one of "CACHE_ON_FAILURE", "CACHE_ALWAYS"
resp.default_run_setting.run_group_id #=> String
resp.default_run_setting.priority #=> Integer
resp.default_run_setting.storage_capacity #=> Integer
resp.default_run_setting.output_uri #=> String
resp.default_run_setting.log_level #=> String, one of "OFF", "FATAL", "ERROR", "ALL"
resp.default_run_setting.run_tags #=> Hash
resp.default_run_setting.run_tags["TagKey"] #=> String
resp.default_run_setting.retention_mode #=> String, one of "RETAIN", "REMOVE"
resp.default_run_setting.storage_type #=> String, one of "STATIC", "DYNAMIC"
resp.default_run_setting.workflow_owner_id #=> String
resp.default_run_setting.output_bucket_owner_id #=> String
resp.default_run_setting.workflow_version_name #=> String
resp.default_run_setting.networking_mode #=> String, one of "RESTRICTED", "VPC"
resp.default_run_setting.configuration_name #=> String
resp.submission_summary.successful_start_submission_count #=> Integer
resp.submission_summary.failed_start_submission_count #=> Integer
resp.submission_summary.pending_start_submission_count #=> Integer
resp.submission_summary.successful_cancel_submission_count #=> Integer
resp.submission_summary.failed_cancel_submission_count #=> Integer
resp.submission_summary.successful_delete_submission_count #=> Integer
resp.submission_summary.failed_delete_submission_count #=> Integer
resp.run_summary.pending_run_count #=> Integer
resp.run_summary.starting_run_count #=> Integer
resp.run_summary.running_run_count #=> Integer
resp.run_summary.stopping_run_count #=> Integer
resp.run_summary.completed_run_count #=> Integer
resp.run_summary.deleted_run_count #=> Integer
resp.run_summary.failed_run_count #=> Integer
resp.run_summary.cancelled_run_count #=> Integer
resp.creation_time #=> Time
resp.submitted_time #=> Time
resp.processed_time #=> Time
resp.failed_time #=> Time
resp.failure_reason #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :batch_id (required, String) —

    The identifier portion of the run batch ARN.

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 2980

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

#get_configuration(params = {}) ⇒ Types::GetConfigurationResponse

Retrieve configuration details for specified name.

Examples:

Request syntax with placeholder values


resp = client.get_configuration({
  name: "ConfigurationName", # required
})

Response structure


resp.arn #=> String
resp.uuid #=> String
resp.name #=> String
resp.description #=> String
resp.run_configurations.vpc_config.security_group_ids #=> Array
resp.run_configurations.vpc_config.security_group_ids[0] #=> String
resp.run_configurations.vpc_config.subnet_ids #=> Array
resp.run_configurations.vpc_config.subnet_ids[0] #=> String
resp.run_configurations.vpc_config.vpc_id #=> String
resp.status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETING", "DELETED", "FAILED"
resp.creation_time #=> Time
resp.tags #=> Hash
resp.tags["TagKey"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    Configuration name to retrieve.

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 3027

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

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

Retrieves detailed information from parts of a read set and returns the read set in the same format that it was uploaded. You must have read sets uploaded to your sequence store in order to run this operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3070

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

Returns detailed information about the status of a read set activation job in JSON format.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3123

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

Retrieves status information about a read set export job and returns the data in JSON format. Use this operation to actively monitor the progress of an 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:



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# File 'lib/aws-sdk-omics/client.rb', line 3179

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 detailed and status information about a read set import job and returns the data in JSON format.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3245

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

Retrieves the metadata for a read set from a sequence store in JSON format. This operation does not return tags. To retrieve the list of tags for a read set, use the ‘ListTagsForResource` API operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3327

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

Downloads parts of data from a reference genome and returns the reference file in the same format that it was uploaded.

For more information, see [Creating a HealthOmics reference store] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/create-reference-store.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3379

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

Monitors the status of a reference import job. This operation can be called after calling the ‘StartReferenceImportJob` operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3439

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

Retrieves metadata for a reference genome. This operation returns the number of parts, part size, and MD5 of an entire file. This operation does not return tags. To retrieve the list of tags for a read set, use the ‘ListTagsForResource` API operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3503

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3542

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/monitoring-cloudwatch-logs.html

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.batch_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
resp.networking_mode #=> String, one of "RESTRICTED", "VPC"
resp.configuration.name #=> String
resp.configuration.arn #=> String
resp.configuration.uuid #=> String
resp.vpc_config.security_group_ids #=> Array
resp.vpc_config.security_group_ids[0] #=> String
resp.vpc_config.subnet_ids #=> Array
resp.vpc_config.subnet_ids[0] #=> String
resp.vpc_config.vpc_id #=> 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:



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# File 'lib/aws-sdk-omics/client.rb', line 3677

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/workflows-call-caching.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3733

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3778

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
resp.image_details.image #=> String
resp.image_details.image_digest #=> String
resp.image_details.source_image #=> 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:



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# File 'lib/aws-sdk-omics/client.rb', line 3848

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3884

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

Retrieves metadata for a sequence store using its ID and returns it in JSON format.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3941

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:



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# File 'lib/aws-sdk-omics/client.rb', line 3978

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

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Gets information about a variant import job.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4045

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Gets information about a variant store.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4113

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/using-get-workflow.html

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", "WDL_LENIENT"
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.container_registry_map.registry_mappings #=> Array
resp.container_registry_map.registry_mappings[0].upstream_registry_url #=> String
resp.container_registry_map.registry_mappings[0].ecr_repository_prefix #=> String
resp.container_registry_map.registry_mappings[0].upstream_repository_prefix #=> String
resp.container_registry_map.registry_mappings[0]. #=> String
resp.container_registry_map.image_mappings #=> Array
resp.container_registry_map.image_mappings[0].source_image #=> String
resp.container_registry_map.image_mappings[0].destination_image #=> 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:



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# File 'lib/aws-sdk-omics/client.rb', line 4228

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][1

in the

*Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/workflow-versions.html

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", "WDL_LENIENT"
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.container_registry_map.registry_mappings #=> Array
resp.container_registry_map.registry_mappings[0].upstream_registry_url #=> String
resp.container_registry_map.registry_mappings[0].ecr_repository_prefix #=> String
resp.container_registry_map.registry_mappings[0].upstream_repository_prefix #=> String
resp.container_registry_map.registry_mappings[0]. #=> String
resp.container_registry_map.image_mappings #=> Array
resp.container_registry_map.image_mappings[0].source_image #=> String
resp.container_registry_map.image_mappings[0].destination_image #=> 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. The ‘workflowId` is not the UUID.

  • :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) —

    The 12-digit account ID of the workflow owner. 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.

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 4347

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Retrieves a list of annotation import jobs.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4416

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4475

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Retrieves a list of annotation stores.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4545

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

#list_batch(params = {}) ⇒ Types::ListBatchResponse

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

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_batch({
  max_items: 1,
  starting_token: "ListToken",
  status: "CREATING", # accepts CREATING, PENDING, SUBMITTING, INPROGRESS, STOPPING, CANCELLED, FAILED, PROCESSED, RUNS_DELETING, RUNS_DELETED
  name: "BatchName",
  run_group_id: "RunGroupId",
})

Response structure


resp.items #=> Array
resp.items[0].id #=> String
resp.items[0].name #=> String
resp.items[0].status #=> String, one of "CREATING", "PENDING", "SUBMITTING", "INPROGRESS", "STOPPING", "CANCELLED", "FAILED", "PROCESSED", "RUNS_DELETING", "RUNS_DELETED"
resp.items[0].created_at #=> Time
resp.items[0].total_runs #=> Integer
resp.items[0].workflow_id #=> String
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_items (Integer) —

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

  • :starting_token (String) —

    A pagination token returned from a prior ‘ListBatch` call.

  • :status (String) —

    Filter batches by status.

  • :name (String) —

    Filter batches by name.

  • :run_group_id (String) —

    Filter batches by run group ID.

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 4602

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

#list_configurations(params = {}) ⇒ Types::ListConfigurationsResponse

List all configurations for the account.

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_configurations({
  max_results: 1,
  starting_token: "ConfigurationListToken",
})

Response structure


resp.items #=> Array
resp.items[0].arn #=> String
resp.items[0].name #=> String
resp.items[0].description #=> String
resp.items[0].status #=> String, one of "CREATING", "ACTIVE", "UPDATING", "DELETING", "DELETED", "FAILED"
resp.items[0].creation_time #=> Time
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

    Maximum number of results to return.

  • :starting_token (String) —

    Pagination token for retrieving next page of results.

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 4643

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

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

Lists in-progress multipart read set uploads for a sequence store and returns it in a JSON formatted output. Multipart read set uploads are initiated by the ‘CreateMultipartReadSetUploads` API operation. This operation returns a response with no body when the upload is complete.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4700

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 and returns the metadata in a JSON formatted output. To extract metadata from a read set activation job, use the ‘GetReadSetActivationJob` API operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4757

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 in a JSON formatted response. This API operation is used to check the status of a read set export job initiated by the ‘StartReadSetExportJob` API operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4814

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 and returns the data in JSON format.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4870

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

Lists all parts in a multipart read set upload for a sequence store and returns the metadata in a JSON formatted output.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 4935

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 from a sequence store ID and returns the metadata in JSON format.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5011

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 the metadata of one or more reference import jobs for a reference 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_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:



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# File 'lib/aws-sdk-omics/client.rb', line 5067

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 linked to your account and returns their metadata in JSON format.

For more information, see [Creating a reference store] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/create-reference-store.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5127

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

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

Retrieves the metadata of one or more reference genomes in a reference store.

For more information, see [Creating a reference store] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/create-reference-store.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5194

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5238

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5288

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5347

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/monitoring-cloudwatch-logs.html

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",
  batch_id: "BatchId",
  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].batch_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.

  • :batch_id (String) —

    Filter by batch 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:



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# File 'lib/aws-sdk-omics/client.rb', line 5424

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

#list_runs_in_batch(params = {}) ⇒ Types::ListRunsInBatchResponse

Returns a paginated list of individual workflow runs within a specific batch. Use this operation to map each ‘runSettingId` to its HealthOmics-generated `runId`, and to check the submission status of each run. Only one filter per call is supported.

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_in_batch({
  batch_id: "BatchId", # required
  max_items: 1,
  starting_token: "ListToken",
  submission_status: "SUCCESS", # accepts SUCCESS, FAILED, CANCEL_SUCCESS, CANCEL_FAILED, DELETE_SUCCESS, DELETE_FAILED
  run_setting_id: "String",
  run_id: "String",
})

Response structure


resp.runs #=> Array
resp.runs[0].run_setting_id #=> String
resp.runs[0].run_id #=> String
resp.runs[0].run_internal_uuid #=> String
resp.runs[0].run_arn #=> String
resp.runs[0].submission_status #=> String, one of "SUCCESS", "FAILED", "CANCEL_SUCCESS", "CANCEL_FAILED", "DELETE_SUCCESS", "DELETE_FAILED"
resp.runs[0].submission_failure_reason #=> String
resp.runs[0].submission_failure_message #=> String
resp.next_token #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :batch_id (required, String) —

    The identifier portion of the run batch ARN.

  • :max_items (Integer) —

    The maximum number of runs to return.

  • :starting_token (String) —

    A pagination token returned from a prior ‘ListRunsInBatch` call.

  • :submission_status (String) —

    Filter runs by submission status.

  • :run_setting_id (String) —

    Filter runs by the customer-provided run setting ID.

  • :run_id (String) —

    Filter runs by the HealthOmics-generated run ID.

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 5486

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

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

Retrieves a list of sequence stores and returns each sequence store’s metadata.

For more information, see [Creating a HealthOmics sequence store] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/create-sequence-store.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5554

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5616

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5645

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Retrieves a list of variant import jobs.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5713

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Retrieves a list of variant stores.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5782

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/workflow-versions.html

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. The ‘workflowId` is not the UUID.

  • :type (String) —

    The workflow type.

  • :workflow_owner_id (String) —

    The 12-digit account ID of the workflow owner. 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.

  • :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:



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# File 'lib/aws-sdk-omics/client.rb', line 5849

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5908

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:



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# File 'lib/aws-sdk-omics/client.rb', line 5948

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Starts an annotation import job.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6034

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 and returns its metadata in a JSON formatted output. AWS HealthOmics automatically archives unused read sets after 30 days. To monitor the status of your read set activation job, use the ‘GetReadSetActivationJob` operation.

To learn more, see [Activating read sets] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/activating-read-sets.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6091

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

Starts a read set export job. When the export job is finished, the read set is exported to an Amazon S3 bucket which can be retrieved using the ‘GetReadSetExportJob` API operation.

To monitor the status of the export job, use the ‘ListReadSetExportJobs` API operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6153

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

Imports a read set from the sequence store. Read set import jobs support a maximum of 100 read sets of different types. Monitor the progress of your read set import job by calling the ‘GetReadSetImportJob` API operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6222

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

Imports a reference genome from Amazon S3 into a specified reference store. You can have multiple reference genomes in a reference store. You can only import reference genomes one at a time into each reference store. Monitor the status of your reference import job by using the ‘GetReferenceImportJob` API operation.

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6284

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][1

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*.

You can use Amazon Q CLI to analyze run logs and make performance optimization recommendations. To get started, see the [Amazon Web Services HealthOmics MCP server] on GitHub.

[1]: docs.aws.amazon.com/omics/latest/dev/starting-a-run.html [2]: docs.aws.amazon.com/omics/latest/dev/run-retention.html [3]: github.com/awslabs/mcp/tree/main/src/aws-healthomics-mcp-server

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", # required
  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",
  networking_mode: "RESTRICTED", # accepts RESTRICTED, VPC
  configuration_name: "ConfigurationName",
})

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
resp.configuration.name #=> String
resp.configuration.arn #=> String
resp.configuration.uuid #=> String
resp.networking_mode #=> 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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/how-run-cache.html#run-cache-behavior

  • :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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/creating-run-groups.html#run-priority

  • :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 (required, 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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/add-a-tag.html

  • :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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/starting-a-run.html

  • :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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/workflows-run-types.html

  • :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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/workflow-versions.html

  • :networking_mode (String) —

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

  • :configuration_name (String) —

    Optional configuration name to use for the workflow run.

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 6568

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

#start_run_batch(params = {}) ⇒ Types::StartRunBatchResponse

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

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

Examples:

Request syntax with placeholder values


resp = client.start_run_batch({
  batch_name: "BatchName",
  request_id: "BatchRequestId", # required
  tags: {
    "TagKey" => "TagValue",
  },
  default_run_setting: { # required
    workflow_id: "WorkflowId", # required
    workflow_type: "PRIVATE", # accepts PRIVATE, READY2RUN
    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
    run_tags: {
      "TagKey" => "TagValue",
    },
    retention_mode: "RETAIN", # accepts RETAIN, REMOVE
    storage_type: "STATIC", # accepts STATIC, DYNAMIC
    workflow_owner_id: "WorkflowOwnerId",
    output_bucket_owner_id: "AwsAccountId",
    workflow_version_name: "WorkflowVersionName",
    networking_mode: "RESTRICTED", # accepts RESTRICTED, VPC
    configuration_name: "ConfigurationName",
  },
  batch_run_settings: { # required
    inline_settings: [
      {
        run_setting_id: "RunSettingId", # required
        name: "RunName",
        output_uri: "RunOutputUri",
        priority: 1,
        parameters: {
        },
        output_bucket_owner_id: "AwsAccountId",
        run_tags: {
          "TagKey" => "TagValue",
        },
      },
    ],
    s3_uri_settings: "S3UriSettings",
  },
})

Response structure


resp.id #=> String
resp.arn #=> String
resp.status #=> String, one of "CREATING", "PENDING", "SUBMITTING", "INPROGRESS", "STOPPING", "CANCELLED", "FAILED", "PROCESSED", "RUNS_DELETING", "RUNS_DELETED"
resp.uuid #=> String
resp.tags #=> Hash
resp.tags["TagKey"] #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :batch_name (String) —

    An optional user-friendly name for the run batch.

  • :request_id (required, String) —

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

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

  • :tags (Hash<String,String>) —

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

  • :default_run_setting (required, Types::DefaultRunSetting) —

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

  • :batch_run_settings (required, Types::BatchRunSettings) —

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

Returns:

See Also:



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# File 'lib/aws-sdk-omics/client.rb', line 6681

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

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Starts a variant import job.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6741

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6769

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6795

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

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Updates an annotation store.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6858

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6908

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/how-run-cache.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 6954

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:



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# File 'lib/aws-sdk-omics/client.rb', line 7013

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:



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# File 'lib/aws-sdk-omics/client.rb', line 7101

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

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

Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [ Amazon Web Services HealthOmics variant store and annotation store availability change].

Updates a variant store.

[1]: docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 7155

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/update-private-workflow.html

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*.

    [1]: docs.aws.amazon.com/omics/latest/dev/Using-workflows.html

  • :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:



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# File 'lib/aws-sdk-omics/client.rb', line 7229

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*.

[1]: docs.aws.amazon.com/omics/latest/dev/workflow-versions.html

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. The ‘workflowId` is not the UUID.

  • :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 version. 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 in the Amazon Web Services HealthOmics User Guide .

    [1]: docs.aws.amazon.com/omics/latest/dev/workflows-run-types.html

  • :storage_capacity (Integer) —

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

  • :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:



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# File 'lib/aws-sdk-omics/client.rb', line 7292

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

Uploads a specific part of a read set into a sequence store. When you a upload a read set part with a part number that already exists, the new part replaces the existing one. This operation returns a JSON formatted response containing a string identifier that is used to confirm that parts are being added to the intended upload.

For more information, see [Direct upload to a sequence store] in the *Amazon Web Services HealthOmics User Guide*.

[1]: docs.aws.amazon.com/omics/latest/dev/synchronous-uploads.html

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:



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# File 'lib/aws-sdk-omics/client.rb', line 7347

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.



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# File 'lib/aws-sdk-omics/client.rb', line 7479

def wait_until(waiter_name, params = {}, options = {})
  w = waiter(waiter_name, options)
  yield(w.waiter) if block_given? # deprecated
  w.wait(params)
end

#waiter_names ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Deprecated. 


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# File 'lib/aws-sdk-omics/client.rb', line 7487

def waiter_names
  waiters.keys
end