Class: Aws::Omics::Client

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

Overview

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

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

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

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

Instance Attribute Summary

Attributes inherited from Seahorse::Client::Base

#config, #handlers

API Operations collapse

Instance Method Summary collapse

Methods included from ClientStubs

#api_requests, #stub_data, #stub_responses

Methods inherited from Seahorse::Client::Base

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

Methods included from Seahorse::Client::HandlerBuilder

#handle, #handle_request, #handle_response

Constructor Details

#initialize(options) ⇒ Client

Returns a new instance of Client.

Parameters:

  • options (Hash)

Options Hash (options):

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

    Your AWS credentials. This can be an instance of any one of the following classes:

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

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

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

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

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

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

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

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

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

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

    • Aws.config[:credentials]
    • The :access_key_id, :secret_access_key, and :session_token options.
    • ENV['AWS_ACCESS_KEY_ID'], ENV['AWS_SECRET_ACCESS_KEY']
    • ~/.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::InstanceProfileCredentails or Aws::ECSCredentials to enable retries and extended timeouts. Instance profile credential fetching can be disabled by setting ENV['AWS_EC2_METADATA_DISABLED'] to true.
  • :region (required, String) —

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

    • Aws.config[:region]
    • ENV['AWS_REGION']
    • ENV['AMAZON_REGION']
    • ENV['AWS_DEFAULT_REGION']
    • ~/.aws/credentials
    • ~/.aws/config
  • :access_key_id (String)
  • :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.

  • :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 —

    Set to true to disable SDK automatically adding host prefix to default service endpoint when available.

  • :endpoint (String) —

    The client endpoint is normally constructed from the :region option. You should only configure an :endpoint when connecting to test or custom endpoints. This should be a valid HTTP(S) URI.

  • :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.

  • :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.

  • :retry_backoff (Proc) —

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

  • :retry_base_delay (Float) — default: 0.3 —

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

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

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

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

  • :retry_limit (Integer) — default: 3 —

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

  • :retry_max_delay (Integer) — default: 0 —

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

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

    Specifies which retry algorithm to use. Values are:

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

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

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

  • :sdk_ua_app_id (String) —

    A unique and opaque application ID that is appended to the User-Agent header as app/. It should have a maximum length of 50.

  • :secret_access_key (String)
  • :session_token (String)
  • :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.

  • :token_provider (Aws::TokenProvider) —

    A Bearer Token Provider. This can be an 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_proxy (URI::HTTP, String) —

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

  • :http_open_timeout (Float) — default: 15 —

    The number of seconds to wait when opening a HTTP session before raising a Timeout::Error.

  • :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_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_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.

  • :ssl_timeout (Float) — default: nil —

    Sets the SSL timeout in seconds.

  • :http_wire_trace (Boolean) — default: false —

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

  • :ssl_verify_peer (Boolean) — default: true —

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

  • :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.



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 370

def initialize(*args)
  super
end

Instance Method Details

#abort_multipart_read_set_upload(params = {}) ⇒ Struct

Stops a multipart upload.

Examples:

Request syntax with placeholder values


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

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

  • :upload_id (required, String) —

    The ID for the multipart upload.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 397

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

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

Deletes one or more read sets.

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :ids (required, Array<String>) —

    The read sets' IDs.

  • :sequence_store_id (required, String) —

    The read sets' sequence store ID.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 432

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

#cancel_annotation_import_job(params = {}) ⇒ Struct

Cancels an annotation import job.

Examples:

Request syntax with placeholder values


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :job_id (required, String) —

    The job's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 454

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.

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 476

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

#cancel_variant_import_job(params = {}) ⇒ Struct

Cancels a variant import job.

Examples:

Request syntax with placeholder values


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :job_id (required, String) —

    The job's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 498

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

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

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

Examples:

Request syntax with placeholder values


resp = client.complete_multipart_read_set_upload({
  sequence_store_id: "SequenceStoreId", # required
  upload_id: "UploadId", # required
  parts: [ # required
    {
      part_number: 1, # required
      part_source: "SOURCE1", # required, accepts SOURCE1, SOURCE2
      checksum: "String", # 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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 541

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

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

Creates an annotation store.

Examples:

Request syntax with placeholder values


resp = client.create_annotation_store({
  reference: {
    reference_arn: "ReferenceArn",
  },
  name: "CreateAnnotationStoreRequestNameString",
  description: "StoreDescription",
  tags: {
    "TagKey" => "TagValue",
  },
  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.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.

  • :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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 629

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

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

Begins a multipart read set upload.

Examples:

Request syntax with placeholder values


resp = client.create_multipart_read_set_upload({
  sequence_store_id: "SequenceStoreId", # required
  client_token: "ClientToken",
  source_file_type: "FASTQ", # required, accepts FASTQ, BAM, CRAM
  subject_id: "SubjectId", # required
  sample_id: "SampleId", # required
  generated_from: "GeneratedFrom",
  reference_arn: "ReferenceArn", # required
  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"
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 (required, 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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 718

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

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

Creates a reference store.

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    A name for the store.

  • :description (String) —

    A description for the store.

  • :sse_config (Types::SseConfig) —

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

  • :tags (Hash<String,String>) —

    Tags for the store.

  • :client_token (String) —

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

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 779

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

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

Creates a 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 to use in the group.

  • :max_runs (Integer) —

    The maximum number of concurrent runs for the group.

  • :max_duration (Integer) —

    A maximum run time for the group in minutes.

  • :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 GPUs that can be used by a run group.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 842

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

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

Creates a sequence store.

Examples:

Request syntax with placeholder values


resp = client.create_sequence_store({
  name: "SequenceStoreName", # required
  description: "SequenceStoreDescription",
  sse_config: {
    type: "KMS", # required, accepts KMS
    key_arn: "SseConfigKeyArnString",
  },
  tags: {
    "TagKey" => "TagValue",
  },
  client_token: "ClientToken",
  fallback_location: "S3Destination",
})

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

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.

  • :fallback_location (String) —

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

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 910

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

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

Creates a variant store.

Examples:

Request syntax with placeholder values


resp = client.create_variant_store({
  reference: { # required
    reference_arn: "ReferenceArn",
  },
  name: "CreateVariantStoreRequestNameString",
  description: "StoreDescription",
  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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 969

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 workflow.

Examples:

Request syntax with placeholder values


resp = client.create_workflow({
  name: "WorkflowName",
  description: "WorkflowDescription",
  engine: "WDL", # accepts WDL, NEXTFLOW
  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
})

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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (String) —

    A name for the workflow.

  • :description (String) —

    A description for the workflow.

  • :engine (String) —

    An engine for the workflow.

  • :definition_zip (String, StringIO, File) —

    A ZIP archive for the workflow.

  • :definition_uri (String) —

    The URI of a definition for the workflow.

  • :main (String) —

    The path of the main definition file for the workflow.

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

    A parameter template for the workflow.

  • :storage_capacity (Integer) —

    A storage capacity for the workflow in gigabytes.

  • :tags (Hash<String,String>) —

    Tags for the workflow.

  • :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.**

  • :accelerators (String) —

    The computational accelerator specified to run the workflow.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1055

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

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

Deletes an annotation store.

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The store's name.

  • :force (Boolean) —

    Whether to force deletion.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1087

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

#delete_reference(params = {}) ⇒ Struct

Deletes a genome reference.

Examples:

Request syntax with placeholder values


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The reference's ID.

  • :reference_store_id (required, String) —

    The reference's store ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1113

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

#delete_reference_store(params = {}) ⇒ Struct

Deletes a genome reference store.

Examples:

Request syntax with placeholder values


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The store's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1135

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

#delete_run(params = {}) ⇒ Struct

Deletes a workflow run.

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1157

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

#delete_run_group(params = {}) ⇒ Struct

Deletes a workflow run group.

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1179

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

#delete_sequence_store(params = {}) ⇒ Struct

Deletes a sequence store.

Examples:

Request syntax with placeholder values


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The sequence store's ID.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1201

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

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

Deletes a variant store.

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The store's name.

  • :force (Boolean) —

    Whether to force deletion.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1233

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.

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1255

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

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

Gets information about an annotation import job.

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

  • annotation_import_job_created

Examples:

Request syntax with placeholder values


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

Response structure


resp.id #=> String
resp.destination_name #=> String
resp.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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1323

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

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

Gets information about an annotation store.

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

  • annotation_store_created
  • annotation_store_deleted

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The store's name.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1390

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

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

Gets a file from a read set.

Examples:

Request syntax with placeholder values


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

Response structure


resp.payload #=> IO

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The read set's ID.

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :file (String) —

    The file to retrieve.

  • :part_number (required, Integer) —

    The part number to retrieve.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1430

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

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

Gets information about a read set activation job.

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

  • read_set_activation_job_completed

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The job's ID.

  • :sequence_store_id (required, String) —

    The job's sequence store ID.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1482

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

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

Gets information about a read set export job.

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

  • read_set_export_job_completed

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The job's sequence store ID.

  • :id (required, String) —

    The job's ID.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1536

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

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

Gets information about a read set import job.

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

  • read_set_import_job_completed

Examples:

Request syntax with placeholder values


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

Response structure


resp.id #=> String
resp.sequence_store_id #=> String
resp.role_arn #=> String
resp.status #=> String, one of "SUBMITTED", "IN_PROGRESS", "CANCELLING", "CANCELLED", "FAILED", "COMPLETED", "COMPLETED_WITH_FAILURES"
resp.status_message #=> String
resp.creation_time #=> Time
resp.completion_time #=> Time
resp.sources #=> Array
resp.sources[0].source_files.source1 #=> String
resp.sources[0].source_files.source2 #=> String
resp.sources[0].source_file_type #=> String, one of "FASTQ", "BAM", "CRAM"
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

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1600

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

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

Gets details about a read set.

Examples:

Request syntax with placeholder values


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

Response structure


resp.id #=> String
resp.arn #=> String
resp.sequence_store_id #=> String
resp.subject_id #=> String
resp.sample_id #=> String
resp.status #=> String, one of "ARCHIVED", "ACTIVATING", "ACTIVE", "DELETING", "DELETED", "PROCESSING_UPLOAD", "UPLOAD_FAILED"
resp.name #=> String
resp.description #=> String
resp.file_type #=> String, one of "FASTQ", "BAM", "CRAM"
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.source2.total_parts #=> Integer
resp.files.source2.part_size #=> Integer
resp.files.source2.content_length #=> Integer
resp.files.index.total_parts #=> Integer
resp.files.index.part_size #=> Integer
resp.files.index.content_length #=> Integer
resp.status_message #=> 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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1669

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

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

Gets a reference file.

Examples:

Request syntax with placeholder values


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

Response structure


resp.payload #=> IO

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The reference's ID.

  • :reference_store_id (required, String) —

    The reference's store ID.

  • :range (String) —

    The range to retrieve.

  • :part_number (required, Integer) —

    The part number to retrieve.

  • :file (String) —

    The file to retrieve.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1713

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

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

Gets information about a reference import job.

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

  • reference_import_job_completed

Examples:

Request syntax with placeholder values


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

Response structure


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

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1771

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

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

Gets information about a genome reference's metadata.

Examples:

Request syntax with placeholder values


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

Response structure


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

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1826

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1865

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

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

Gets information about a workflow run.

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.status #=> String, one of "PENDING", "STARTING", "RUNNING", "STOPPING", "COMPLETED", "DELETED", "CANCELLED", "FAILED"
resp.workflow_id #=> String
resp.workflow_type #=> String, one of "PRIVATE", "READY2RUN"
resp.run_id #=> String
resp.role_arn #=> String
resp.name #=> String
resp.run_group_id #=> String
resp.priority #=> Integer
resp.definition #=> String
resp.digest #=> String
resp.storage_capacity #=> Integer
resp.output_uri #=> String
resp.log_level #=> String, one of "OFF", "FATAL", "ERROR", "ALL"
resp.resource_digests #=> Hash
resp.resource_digests["RunResourceDigestKey"] #=> String
resp.started_by #=> String
resp.creation_time #=> Time
resp.start_time #=> Time
resp.stop_time #=> Time
resp.status_message #=> String
resp.tags #=> Hash
resp.tags["TagKey"] #=> String
resp.accelerators #=> String, one of "GPU"

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1950

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

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

Gets information about a workflow run group.

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 1995

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 information about a workflow run task.

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.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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The task's ID.

  • :task_id (required, String) —

    The task's ID.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2053

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

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

Gets information about a sequence store.

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :id (required, String) —

    The store's ID.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2094

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

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

Gets information about a variant import job.

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

  • variant_import_job_created

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :job_id (required, String) —

    The job's ID.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2151

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

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

Gets information about a variant store.

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

  • variant_store_created
  • variant_store_deleted

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (required, String) —

    The store's name.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2209

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

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

Gets information about a workflow.

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
})

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"
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"

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.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2286

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

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

Retrieves a list of annotation import jobs.

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

Examples:

Request syntax with placeholder values


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

Response structure


resp.annotation_import_jobs #=> Array
resp.annotation_import_jobs[0].id #=> String
resp.annotation_import_jobs[0].destination_name #=> String
resp.annotation_import_jobs[0].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) —

    Specify 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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2344

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

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

Retrieves a list of annotation stores.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :ids (Array<String>) —

    IDs of stores to list.

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ListAnnotationStoresFilter) —

    A filter to apply to the list.

Returns:

See Also:



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

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

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

Lists all multipart read set uploads and their statuses.

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"
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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2458

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

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

Retrieves a list of read set activation jobs.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ActivateReadSetFilter) —

    A filter to apply to the list.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2513

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

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

Retrieves a list of read set export jobs.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The jobs' sequence store ID.

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ExportReadSetFilter) —

    A filter to apply to the list.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2568

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

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

Retrieves a list of read set import jobs.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :sequence_store_id (required, String) —

    The jobs' sequence store ID.

  • :filter (Types::ImportReadSetFilter) —

    A filter to apply to the list.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2623

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

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

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

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The Sequence Store ID used for the multipart uploads.

  • :upload_id (required, String) —

    The ID for the initiated multipart upload.

  • :part_source (required, String) —

    The source file for the upload part.

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ReadSetUploadPartListFilter) —

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

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2688

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

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

Retrieves a list of read sets.

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

Examples:

Request syntax with placeholder values


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

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"
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

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2758

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

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

Retrieves a list of reference import jobs.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :reference_store_id (required, String) —

    The job's reference store ID.

  • :filter (Types::ImportReferenceFilter) —

    A filter to apply to the list.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2813

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

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

Retrieves a list of reference stores.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ReferenceStoreFilter) —

    A filter to apply to the list.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2865

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

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

Retrieves a list of references.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :reference_store_id (required, String) —

    The references' reference store ID.

  • :max_results (Integer) —

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

  • :next_token (String) —

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

  • :filter (Types::ReferenceFilter) —

    A filter to apply to the list.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2924

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

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

Retrieves a list of run groups.

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 2973

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

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

Retrieves a list of tasks for a run.

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].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.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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3027

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.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :name (String) —

    Filter the list by run name.

  • :run_group_id (String) —

    Filter the list by run group ID.

  • :starting_token (String) —

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

  • :max_results (Integer) —

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

  • :status (String) —

    The status of a run.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3086

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

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

Retrieves a list of sequence stores.

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

Examples:

Request syntax with placeholder values


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

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

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3139

def list_sequence_stores(params = {}, options = {})
  req = build_request(:list_sequence_stores, 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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3168

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

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

Retrieves a list of variant import jobs.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :ids (Array<String>) —

    A list of job IDs.

  • :next_token (String) —

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

  • :filter (Types::ListVariantImportJobsFilter) —

    A filter to apply to the list.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3226

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

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

Retrieves a list of variant stores.

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :max_results (Integer) —

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

  • :ids (Array<String>) —

    A list of store IDs.

  • :next_token (String) —

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

  • :filter (Types::ListVariantStoresFilter) —

    A filter to apply to the list.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3285

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

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

Retrieves a list of 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) —

    The workflows' type.

  • :name (String) —

    The workflows' 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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3339

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

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

Starts an annotation import job.

Examples:

Request syntax with placeholder values


resp = client.start_annotation_import_job({
  destination_name: "StoreName", # required
  role_arn: "Arn", # required
  items: [ # required
    {
      source: "S3Uri", # required
    },
  ],
  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.

  • :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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3411

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

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

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

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :client_token (String) —

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

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

    The job's source files.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3459

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

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

Exports a read set to Amazon S3.

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The read set's sequence store ID.

  • :destination (required, String) —

    A location for exported files in Amazon S3.

  • :role_arn (required, String) —

    A service role for the job.

  • :client_token (String) —

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

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

    The job's source files.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3516

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

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

Starts a read set import job.

Examples:

Request syntax with placeholder values


resp = client.start_read_set_import_job({
  sequence_store_id: "SequenceStoreId", # required
  role_arn: "RoleArn", # required
  client_token: "ClientToken",
  sources: [ # required
    {
      source_files: { # required
        source1: "S3Uri", # required
        source2: "S3Uri",
      },
      source_file_type: "FASTQ", # required, accepts FASTQ, BAM, CRAM
      subject_id: "SubjectId", # required
      sample_id: "SampleId", # required
      generated_from: "GeneratedFrom",
      reference_arn: "ReferenceArn", # required
      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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3582

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

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

Starts a reference import job.

Examples:

Request syntax with placeholder values


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

Response structure


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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :reference_store_id (required, String) —

    The job's reference store ID.

  • :role_arn (required, String) —

    A service role for the job.

  • :client_token (String) —

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

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

    The job's source files.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3640

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 run.

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",
  run_group_id: "RunGroupId",
  priority: 1,
  parameters: {
  },
  storage_capacity: 1,
  output_uri: "RunOutputUri",
  log_level: "OFF", # accepts OFF, FATAL, ERROR, ALL
  tags: {
    "TagKey" => "TagValue",
  },
  request_id: "RunRequestId", # required
})

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

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :workflow_id (String) —

    The run's workflow ID.

  • :workflow_type (String) —

    The run's workflows type.

  • :run_id (String) —

    The run's ID.

  • :role_arn (required, String) —

    A service role for the run.

  • :name (String) —

    A name for the run.

  • :run_group_id (String) —

    The run's group ID.

  • :priority (Integer) —

    A priority for the run.

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

    Parameters for the run.

    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) —

    A storage capacity for the run in gigabytes.

  • :output_uri (String) —

    An output URI for the run.

  • :log_level (String) —

    A log level for the run.

  • :tags (Hash<String,String>) —

    Tags for the run.

  • :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.**

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3735

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

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

Starts a variant import job.

Examples:

Request syntax with placeholder values


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

Response structure


resp.job_id #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :destination_name (required, String) —

    The destination variant store for the job.

  • :role_arn (required, String) —

    A service role for the job.

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

    Items to import.

  • :run_left_normalization (Boolean) —

    The job's left normalization setting.

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

    The annotation schema generated by the parsed annotation data.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3785

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3813

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3839

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

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

Updates an annotation store.

Examples:

Request syntax with placeholder values


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

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3892

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

#update_run_group(params = {}) ⇒ Struct

Updates a run group.

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 3934

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

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

Updates a variant store.

Examples:

Request syntax with placeholder values


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

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

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

#update_workflow(params = {}) ⇒ Struct

Updates a workflow.

Examples:

Request syntax with placeholder values


resp = client.update_workflow({
  id: "WorkflowId", # required
  name: "WorkflowName",
  description: "WorkflowDescription",
})

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.

Returns:

  • (Struct) —

    Returns an empty response.

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4008

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

#upload_read_set_part(params = {}) ⇒ Types::UploadReadSetPartResponse

This operation uploads a specific part of a read set. If you upload a new part using a previously used part number, the previously uploaded part will be overwritten.

Examples:

Request syntax with placeholder values


resp = client.upload_read_set_part({
  sequence_store_id: "SequenceStoreId", # required
  upload_id: "UploadId", # required
  part_source: "SOURCE1", # required, accepts SOURCE1, SOURCE2
  part_number: 1, # required
  payload: "data", # required
})

Response structure


resp.checksum #=> String

Parameters:

  • params (Hash) (defaults to: {}) —

    ({})

Options Hash (params):

  • :sequence_store_id (required, String) —

    The Sequence Store ID used for the multipart upload.

  • :upload_id (required, String) —

    The ID for the initiated multipart upload.

  • :part_source (required, String) —

    The source file for an upload part.

  • :part_number (required, Integer) —

    The number of the part being uploaded.

  • :payload (required, String, IO) —

    The read set data to upload for a part.

Returns:

See Also:



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# File 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4054

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
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

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 'gems/aws-sdk-omics/lib/aws-sdk-omics/client.rb', line 4178

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