R/omics_service.R

In paws.storage: 'Amazon Web Services' Storage Services

# This file is generated by make.paws. Please do not edit here.
#' @importFrom paws.common new_handlers new_service set_config merge_config
NULL

#' Amazon Omics
#'
#' @description
#' Amazon Web Services HealthOmics is a service that helps users such as bioinformaticians, researchers, and scientists to store, query, analyze, and generate insights from genomics and other biological data. It simplifies and accelerates the process of storing and analyzing genomic information for Amazon Web Services.
#' 
#' For an introduction to the service, see [What is Amazon Web Services HealthOmics?](https://docs.aws.amazon.com/omics/latest/dev/what-is-healthomics.html) in the *Amazon Web Services HealthOmics User Guide*.
#'
#' @param
#' config
#' Optional configuration of credentials, endpoint, and/or region.
#' \itemize{
#' \item{\strong{credentials}: \itemize{
#' \item{\strong{creds}: \itemize{
#' \item{\strong{access_key_id}: AWS access key ID}
#' \item{\strong{secret_access_key}: AWS secret access key}
#' \item{\strong{session_token}: AWS temporary session token}
#' }}
#' \item{\strong{profile}: The name of a profile to use. If not given, then the default profile is used.}
#' \item{\strong{anonymous}: Set anonymous credentials.}
#' }}
#' \item{\strong{endpoint}: The complete URL to use for the constructed client.}
#' \item{\strong{region}: The AWS Region used in instantiating the client.}
#' \item{\strong{close_connection}: Immediately close all HTTP connections.}
#' \item{\strong{timeout}: The time in seconds till a timeout exception is thrown when attempting to make a connection. The default is 60 seconds.}
#' \item{\strong{s3_force_path_style}: Set this to `true` to force the request to use path-style addressing, i.e. `http://s3.amazonaws.com/BUCKET/KEY`.}
#' \item{\strong{sts_regional_endpoint}: Set sts regional endpoint resolver to regional or legacy \url{https://docs.aws.amazon.com/sdkref/latest/guide/feature-sts-regionalized-endpoints.html}}
#' }
#' @param
#' credentials
#' Optional credentials shorthand for the config parameter
#' \itemize{
#' \item{\strong{creds}: \itemize{
#' \item{\strong{access_key_id}: AWS access key ID}
#' \item{\strong{secret_access_key}: AWS secret access key}
#' \item{\strong{session_token}: AWS temporary session token}
#' }}
#' \item{\strong{profile}: The name of a profile to use. If not given, then the default profile is used.}
#' \item{\strong{anonymous}: Set anonymous credentials.}
#' }
#' @param
#' endpoint
#' Optional shorthand for complete URL to use for the constructed client.
#' @param
#' region
#' Optional shorthand for AWS Region used in instantiating the client.
#'
#' @section Service syntax:
#' ```
#' svc <- omics(
#'   config = list(
#'     credentials = list(
#'       creds = list(
#'         access_key_id = "string",
#'         secret_access_key = "string",
#'         session_token = "string"
#'       ),
#'       profile = "string",
#'       anonymous = "logical"
#'     ),
#'     endpoint = "string",
#'     region = "string",
#'     close_connection = "logical",
#'     timeout = "numeric",
#'     s3_force_path_style = "logical",
#'     sts_regional_endpoint = "string"
#'   ),
#'   credentials = list(
#'     creds = list(
#'       access_key_id = "string",
#'       secret_access_key = "string",
#'       session_token = "string"
#'     ),
#'     profile = "string",
#'     anonymous = "logical"
#'   ),
#'   endpoint = "string",
#'   region = "string"
#' )
#' ```
#'
#' @examples
#' \dontrun{
#' svc <- omics()
#' svc$abort_multipart_read_set_upload(
#'   Foo = 123
#' )
#' }
#'
#' @section Operations:
#' \tabular{ll}{
#'  \link[=omics_abort_multipart_read_set_upload]{abort_multipart_read_set_upload} \tab Stops a multipart read set upload into a sequence store and returns a response with no body if the operation is successful\cr
#'  \link[=omics_accept_share]{accept_share} \tab Accept a resource share request\cr
#'  \link[=omics_batch_delete_read_set]{batch_delete_read_set} \tab Deletes one or more read sets\cr
#'  \link[=omics_cancel_annotation_import_job]{cancel_annotation_import_job} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_cancel_run]{cancel_run} \tab Cancels a run using its ID and returns a response with no body if the operation is successful\cr
#'  \link[=omics_cancel_run_batch]{cancel_run_batch} \tab Cancels all runs within a specified batch\cr
#'  \link[=omics_cancel_variant_import_job]{cancel_variant_import_job} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_complete_multipart_read_set_upload]{complete_multipart_read_set_upload} \tab Completes a multipart read set upload into a sequence store after you have initiated the upload process with CreateMultipartReadSetUpload and uploaded all read set parts using UploadReadSetPart\cr
#'  \link[=omics_create_annotation_store]{create_annotation_store} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_create_annotation_store_version]{create_annotation_store_version} \tab Creates a new version of an annotation store\cr
#'  \link[=omics_create_configuration]{create_configuration} \tab Create a new configuration\cr
#'  \link[=omics_create_multipart_read_set_upload]{create_multipart_read_set_upload} \tab Initiates a multipart read set upload for uploading partitioned source files into a sequence store\cr
#'  \link[=omics_create_reference_store]{create_reference_store} \tab Creates a reference store and returns metadata in JSON format\cr
#'  \link[=omics_create_run_cache]{create_run_cache} \tab Creates a run cache to store and reference task outputs from completed private runs\cr
#'  \link[=omics_create_run_group]{create_run_group} \tab Creates a run group to limit the compute resources for the runs that are added to the group\cr
#'  \link[=omics_create_sequence_store]{create_sequence_store} \tab Creates a sequence store and returns its metadata\cr
#'  \link[=omics_create_share]{create_share} \tab Creates a cross-account shared resource\cr
#'  \link[=omics_create_variant_store]{create_variant_store} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_create_workflow]{create_workflow} \tab Creates a private workflow\cr
#'  \link[=omics_create_workflow_version]{create_workflow_version} \tab Creates a new workflow version for the workflow that you specify with the workflowId parameter\cr
#'  \link[=omics_delete_annotation_store]{delete_annotation_store} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_delete_annotation_store_versions]{delete_annotation_store_versions} \tab Deletes one or multiple versions of an annotation store\cr
#'  \link[=omics_delete_batch]{delete_batch} \tab Deletes a run batch resource and its associated metadata\cr
#'  \link[=omics_delete_configuration]{delete_configuration} \tab Delete an existing configuration\cr
#'  \link[=omics_delete_reference]{delete_reference} \tab Deletes a reference genome and returns a response with no body if the operation is successful\cr
#'  \link[=omics_delete_reference_store]{delete_reference_store} \tab Deletes a reference store and returns a response with no body if the operation is successful\cr
#'  \link[=omics_delete_run]{delete_run} \tab Deletes a run and returns a response with no body if the operation is successful\cr
#'  \link[=omics_delete_run_batch]{delete_run_batch} \tab Deletes the individual workflow runs within a batch\cr
#'  \link[=omics_delete_run_cache]{delete_run_cache} \tab Deletes a run cache and returns a response with no body if the operation is successful\cr
#'  \link[=omics_delete_run_group]{delete_run_group} \tab Deletes a run group and returns a response with no body if the operation is successful\cr
#'  \link[=omics_delete_s3_access_policy]{delete_s3_access_policy} \tab Deletes an access policy for the specified store\cr
#'  \link[=omics_delete_sequence_store]{delete_sequence_store} \tab Deletes a sequence store and returns a response with no body if the operation is successful\cr
#'  \link[=omics_delete_share]{delete_share} \tab Deletes a resource share\cr
#'  \link[=omics_delete_variant_store]{delete_variant_store} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_delete_workflow]{delete_workflow} \tab Deletes a workflow by specifying its ID\cr
#'  \link[=omics_delete_workflow_version]{delete_workflow_version} \tab Deletes a workflow version\cr
#'  \link[=omics_get_annotation_import_job]{get_annotation_import_job} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_get_annotation_store]{get_annotation_store} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_get_annotation_store_version]{get_annotation_store_version} \tab Retrieves the metadata for an annotation store version\cr
#'  \link[=omics_get_batch]{get_batch} \tab Retrieves details and current status for a specific run batch, including submission progress and run execution counts\cr
#'  \link[=omics_get_configuration]{get_configuration} \tab Retrieve configuration details for specified name\cr
#'  \link[=omics_get_read_set]{get_read_set} \tab Retrieves detailed information from parts of a read set and returns the read set in the same format that it was uploaded\cr
#'  \link[=omics_get_read_set_activation_job]{get_read_set_activation_job} \tab Returns detailed information about the status of a read set activation job in JSON format\cr
#'  \link[=omics_get_read_set_export_job]{get_read_set_export_job} \tab Retrieves status information about a read set export job and returns the data in JSON format\cr
#'  \link[=omics_get_read_set_import_job]{get_read_set_import_job} \tab Gets detailed and status information about a read set import job and returns the data in JSON format\cr
#'  \link[=omics_get_read_set_metadata]{get_read_set_metadata} \tab Retrieves the metadata for a read set from a sequence store in JSON format\cr
#'  \link[=omics_get_reference]{get_reference} \tab Downloads parts of data from a reference genome and returns the reference file in the same format that it was uploaded\cr
#'  \link[=omics_get_reference_import_job]{get_reference_import_job} \tab Monitors the status of a reference import job\cr
#'  \link[=omics_get_reference_metadata]{get_reference_metadata} \tab Retrieves metadata for a reference genome\cr
#'  \link[=omics_get_reference_store]{get_reference_store} \tab Gets information about a reference store\cr
#'  \link[=omics_get_run]{get_run} \tab Gets detailed information about a specific run using its ID\cr
#'  \link[=omics_get_run_cache]{get_run_cache} \tab Retrieves detailed information about the specified run cache using its ID\cr
#'  \link[=omics_get_run_group]{get_run_group} \tab Gets information about a run group and returns its metadata\cr
#'  \link[=omics_get_run_task]{get_run_task} \tab Gets detailed information about a run task using its ID\cr
#'  \link[=omics_get_s3_access_policy]{get_s3_access_policy} \tab Retrieves details about an access policy on a given store\cr
#'  \link[=omics_get_sequence_store]{get_sequence_store} \tab Retrieves metadata for a sequence store using its ID and returns it in JSON format\cr
#'  \link[=omics_get_share]{get_share} \tab Retrieves the metadata for the specified resource share\cr
#'  \link[=omics_get_variant_import_job]{get_variant_import_job} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_get_variant_store]{get_variant_store} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_get_workflow]{get_workflow} \tab Gets all information about a workflow using its ID\cr
#'  \link[=omics_get_workflow_version]{get_workflow_version} \tab Gets information about a workflow version\cr
#'  \link[=omics_list_annotation_import_jobs]{list_annotation_import_jobs} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_list_annotation_stores]{list_annotation_stores} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_list_annotation_store_versions]{list_annotation_store_versions} \tab Lists the versions of an annotation store\cr
#'  \link[=omics_list_batch]{list_batch} \tab Returns a list of run batches in your account, with optional filtering by status, name, or run group\cr
#'  \link[=omics_list_configurations]{list_configurations} \tab List all configurations for the account\cr
#'  \link[=omics_list_multipart_read_set_uploads]{list_multipart_read_set_uploads} \tab Lists in-progress multipart read set uploads for a sequence store and returns it in a JSON formatted output\cr
#'  \link[=omics_list_read_set_activation_jobs]{list_read_set_activation_jobs} \tab Retrieves a list of read set activation jobs and returns the metadata in a JSON formatted output\cr
#'  \link[=omics_list_read_set_export_jobs]{list_read_set_export_jobs} \tab Retrieves a list of read set export jobs in a JSON formatted response\cr
#'  \link[=omics_list_read_set_import_jobs]{list_read_set_import_jobs} \tab Retrieves a list of read set import jobs and returns the data in JSON format\cr
#'  \link[=omics_list_read_sets]{list_read_sets} \tab Retrieves a list of read sets from a sequence store ID and returns the metadata in JSON format\cr
#'  \link[=omics_list_read_set_upload_parts]{list_read_set_upload_parts} \tab Lists all parts in a multipart read set upload for a sequence store and returns the metadata in a JSON formatted output\cr
#'  \link[=omics_list_reference_import_jobs]{list_reference_import_jobs} \tab Retrieves the metadata of one or more reference import jobs for a reference store\cr
#'  \link[=omics_list_references]{list_references} \tab Retrieves the metadata of one or more reference genomes in a reference store\cr
#'  \link[=omics_list_reference_stores]{list_reference_stores} \tab Retrieves a list of reference stores linked to your account and returns their metadata in JSON format\cr
#'  \link[=omics_list_run_caches]{list_run_caches} \tab Retrieves a list of your run caches and the metadata for each cache\cr
#'  \link[=omics_list_run_groups]{list_run_groups} \tab Retrieves a list of all run groups and returns the metadata for each run group\cr
#'  \link[=omics_list_runs]{list_runs} \tab Retrieves a list of runs and returns each run's metadata and status\cr
#'  \link[=omics_list_runs_in_batch]{list_runs_in_batch} \tab Returns a paginated list of individual workflow runs within a specific batch\cr
#'  \link[=omics_list_run_tasks]{list_run_tasks} \tab Returns a list of tasks and status information within their specified run\cr
#'  \link[=omics_list_sequence_stores]{list_sequence_stores} \tab Retrieves a list of sequence stores and returns each sequence store's metadata\cr
#'  \link[=omics_list_shares]{list_shares} \tab Retrieves the resource shares associated with an account\cr
#'  \link[=omics_list_tags_for_resource]{list_tags_for_resource} \tab Retrieves a list of tags for a resource\cr
#'  \link[=omics_list_variant_import_jobs]{list_variant_import_jobs} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_list_variant_stores]{list_variant_stores} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_list_workflows]{list_workflows} \tab Retrieves a list of existing workflows\cr
#'  \link[=omics_list_workflow_versions]{list_workflow_versions} \tab Lists the workflow versions for the specified workflow\cr
#'  \link[=omics_put_s3_access_policy]{put_s3_access_policy} \tab Adds an access policy to the specified store\cr
#'  \link[=omics_start_annotation_import_job]{start_annotation_import_job} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_start_read_set_activation_job]{start_read_set_activation_job} \tab Activates an archived read set and returns its metadata in a JSON formatted output\cr
#'  \link[=omics_start_read_set_export_job]{start_read_set_export_job} \tab Starts a read set export job\cr
#'  \link[=omics_start_read_set_import_job]{start_read_set_import_job} \tab Imports a read set from the sequence store\cr
#'  \link[=omics_start_reference_import_job]{start_reference_import_job} \tab Imports a reference genome from Amazon S3 into a specified reference store\cr
#'  \link[=omics_start_run]{start_run} \tab Starts a new run and returns details about the run, or duplicates an existing run\cr
#'  \link[=omics_start_run_batch]{start_run_batch} \tab Starts a batch of workflow runs\cr
#'  \link[=omics_start_variant_import_job]{start_variant_import_job} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_tag_resource]{tag_resource} \tab Tags a resource\cr
#'  \link[=omics_untag_resource]{untag_resource} \tab Removes tags from a resource\cr
#'  \link[=omics_update_annotation_store]{update_annotation_store} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_update_annotation_store_version]{update_annotation_store_version} \tab Updates the description of an annotation store version\cr
#'  \link[=omics_update_run_cache]{update_run_cache} \tab Updates a run cache using its ID and returns a response with no body if the operation is successful\cr
#'  \link[=omics_update_run_group]{update_run_group} \tab Updates the settings of a run group and returns a response with no body if the operation is successful\cr
#'  \link[=omics_update_sequence_store]{update_sequence_store} \tab Update one or more parameters for the sequence store\cr
#'  \link[=omics_update_variant_store]{update_variant_store} \tab Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers\cr
#'  \link[=omics_update_workflow]{update_workflow} \tab Updates information about a workflow\cr
#'  \link[=omics_update_workflow_version]{update_workflow_version} \tab Updates information about the workflow version\cr
#'  \link[=omics_upload_read_set_part]{upload_read_set_part} \tab Uploads a specific part of a read set into a sequence store
#' }
#'
#' @return
#' A client for the service. You can call the service's operations using
#' syntax like `svc$operation(...)`, where `svc` is the name you've assigned
#' to the client. The available operations are listed in the
#' Operations section.
#'
#' @rdname omics
#' @export
omics <- function(config = list(), credentials = list(), endpoint = NULL, region = NULL) {
  config <- merge_config(
    config,
    list(
      credentials = credentials,
      endpoint = endpoint,
      region = region
    )
  )
  svc <- .omics$operations
  svc <- set_config(svc, config)
  return(svc)
}

# Private API objects: metadata, handlers, interfaces, etc.
.omics <- list()

.omics$operations <- list()

.omics$metadata <- list(
  service_name = "omics",
  endpoints = list("^(us|eu|ap|sa|ca|me|af|il|mx)\\-\\w+\\-\\d+$" = list(endpoint = "omics.{region}.amazonaws.com", global = FALSE), "^cn\\-\\w+\\-\\d+$" = list(endpoint = "omics.{region}.amazonaws.com.cn", global = FALSE), "^us\\-gov\\-\\w+\\-\\d+$" = list(endpoint = "omics.{region}.amazonaws.com", global = FALSE), "^us\\-iso\\-\\w+\\-\\d+$" = list(endpoint = "omics.{region}.c2s.ic.gov", global = FALSE), "^us\\-isob\\-\\w+\\-\\d+$" = list(endpoint = "omics.{region}.sc2s.sgov.gov", global = FALSE), "^eu\\-isoe\\-\\w+\\-\\d+$" = list(endpoint = "omics.{region}.cloud.adc-e.uk", global = FALSE), "^us\\-isof\\-\\w+\\-\\d+$" = list(endpoint = "omics.{region}.csp.hci.ic.gov", global = FALSE), "^eusc\\-(de)\\-\\w+\\-\\d+$" = list(endpoint = "omics.{region}.amazonaws.eu", global = FALSE)),
  service_id = "Omics",
  api_version = "2022-11-28",
  signing_name = "omics",
  json_version = "",
  target_prefix = ""
)

.omics$service <- function(config = list(), op = NULL) {
  handlers <- new_handlers("restjson", "v4")
  new_service(.omics$metadata, handlers, config, op)
}