/// <summary>
/// Updates a call set. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This method supports patch semantics.
/// Documentation https://developers.google.com/genomics/v1/reference/callsets/patch
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="callSetId">The ID of the call set to be updated.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <param name="optional">Optional paramaters.</param> /// <returns>CallSetResponse</returns>
public static CallSet Patch(genomicsService service, string callSetId, CallSet body, CallsetsPatchOptionalParms optional = null)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
if (callSetId == null)
{
throw new ArgumentNullException(callSetId);
}
// Building the initial request.
var request = service.Callsets.Patch(body, callSetId);
// Applying optional parameters to the request.
request = (CallsetsResource.PatchRequest)SampleHelpers.ApplyOptionalParms(request, optional);
// Requesting data.
return(request.Execute());
}
catch (Exception ex)
{
throw new Exception("Request Callsets.Patch failed.", ex);
}
}
/// <summary>
/// Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation.
/// Documentation https://developers.google.com/genomics/v1/reference/operations/cancel
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="name">The name of the operation resource to be cancelled.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <returns>EmptyResponse</returns>
public static Empty Cancel(genomicsService service, string name, CancelOperationRequest body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
if (name == null)
{
throw new ArgumentNullException(name);
}
// Make the request.
return(service.Operations.Cancel(body, name).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Operations.Cancel failed.", ex);
}
}
/// <summary>
/// Undeletes a dataset by restoring a dataset which was deleted via this API. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This operation is only possible for a week after the deletion occurred.
/// Documentation https://developers.google.com/genomics/v1/reference/datasets/undelete
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="datasetId">The ID of the dataset to be undeleted.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <returns>DatasetResponse</returns>
public static Dataset Undelete(genomicsService service, string datasetId, UndeleteDatasetRequest body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
if (datasetId == null)
{
throw new ArgumentNullException(datasetId);
}
// Make the request.
return(service.Datasets.Undelete(body, datasetId).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Datasets.Undelete failed.", ex);
}
}
/// <summary>
/// Returns permissions that a caller has on the specified resource. See Testing Permissions for more information. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
/// Documentation https://developers.google.com/genomics/v1/reference/datasets/testIamPermissions
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="resource">REQUIRED: The resource for which policy is being specified. Format is `datasets/`.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <returns>TestIamPermissionsResponseResponse</returns>
public static TestIamPermissionsResponse TestIamPermissions(genomicsService service, string resource, TestIamPermissionsRequest body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
if (resource == null)
{
throw new ArgumentNullException(resource);
}
// Make the request.
return(service.Datasets.TestIamPermissions(body, resource).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Datasets.TestIamPermissions failed.", ex);
}
}
/// <summary>
/// Updates an annotation set. The update must respect all mutability restrictions and other invariants described on the annotation set resource. Caller must have WRITE permission for the associated dataset.
/// Documentation https://developers.google.com/genomics/v1/reference/annotationsets/update
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="annotationSetId">The ID of the annotation set to be updated.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <param name="optional">Optional paramaters.</param> /// <returns>AnnotationSetResponse</returns>
public static AnnotationSet Update(genomicsService service, string annotationSetId, AnnotationSet body, AnnotationsetsUpdateOptionalParms optional = null)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
if (annotationSetId == null)
{
throw new ArgumentNullException(annotationSetId);
}
// Building the initial request.
var request = service.Annotationsets.Update(body, annotationSetId);
// Applying optional parameters to the request.
request = (AnnotationsetsResource.UpdateRequest)SampleHelpers.ApplyOptionalParms(request, optional);
// Requesting data.
return(request.Execute());
}
catch (Exception ex)
{
throw new Exception("Request Annotationsets.Update failed.", ex);
}
}
/// <summary>
/// Lists operations that match the specified filter in the request.
/// Documentation https://developers.google.com/genomics/v1/reference/operations/list
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="name">The name of the operation collection.</param>
/// <param name="optional">Optional paramaters.</param> /// <returns>ListOperationsResponseResponse</returns>
public static ListOperationsResponse List(genomicsService service, string name, OperationsListOptionalParms optional = null)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (name == null)
{
throw new ArgumentNullException(name);
}
// Building the initial request.
var request = service.Operations.List(name);
// Applying optional parameters to the request.
request = (OperationsResource.ListRequest)SampleHelpers.ApplyOptionalParms(request, optional);
// Requesting data.
return(request.Execute());
}
catch (Exception ex)
{
throw new Exception("Request Operations.List failed.", ex);
}
}
/// <summary>
/// Exports variant set data to an external destination. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
/// Documentation https://developers.google.com/genomics/v1/reference/variantsets/export
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="variantSetId">Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <returns>OperationResponse</returns>
public static Operation Export(genomicsService service, string variantSetId, ExportVariantSetRequest body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
if (variantSetId == null)
{
throw new ArgumentNullException(variantSetId);
}
// Make the request.
return(service.Variantsets.Export(body, variantSetId).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Variantsets.Export failed.", ex);
}
}
/// <summary>
/// Gets the latest state of a long-running operation. Clients can use this method to poll the operation result at intervals as recommended by the API service.
/// Documentation https://developers.google.com/genomics/v1/reference/operations/get
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="name">The name of the operation resource.</param>
/// <returns>OperationResponse</returns>
public static Operation Get(genomicsService service, string name)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (name == null)
{
throw new ArgumentNullException(name);
}
// Make the request.
return(service.Operations.Get(name).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Operations.Get failed.", ex);
}
}
/// <summary>
/// Runs a pipeline. If `pipelineId` is specified in the request, then run a saved pipeline. If `ephemeralPipeline` is specified, then run that pipeline once without saving a copy. The caller must have READ permission to the project where the pipeline is stored and WRITE permission to the project where the pipeline will be run, as VMs will be created and storage will be used.
/// Documentation https://developers.google.com/genomics/v1alpha2/reference/pipelines/run
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="body">A valid genomics v1alpha2 body.</param>
/// <returns>OperationResponse</returns>
public static Operation Run(genomicsService service, RunPipelineRequest body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
// Make the request.
return(service.Pipelines.Run(body).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Pipelines.Run failed.", ex);
}
}
/// <summary>
/// Gets an annotation. Caller must have READ permission for the associated annotation set.
/// Documentation https://developers.google.com/genomics/v1/reference/annotations/get
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="annotationId">The ID of the annotation to be retrieved.</param>
/// <returns>AnnotationResponse</returns>
public static Annotation Get(genomicsService service, string annotationId)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (annotationId == null)
{
throw new ArgumentNullException(annotationId);
}
// Make the request.
return(service.Annotations.Get(annotationId).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Annotations.Get failed.", ex);
}
}
/// <summary>
/// Gets a list of variants matching the criteria. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
/// Documentation https://developers.google.com/genomics/v1/reference/variants/search
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <returns>SearchVariantsResponseResponse</returns>
public static SearchVariantsResponse Search(genomicsService service, SearchVariantsRequest body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
// Make the request.
return(service.Variants.Search(body).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Variants.Search failed.", ex);
}
}
/// <summary>
/// Returns a stream of all the reads matching the search request, ordered by reference name, position, and ID.
/// Documentation https://developers.google.com/genomics/v1/reference/reads/stream
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <returns>StreamReadsResponseResponse</returns>
public static StreamReadsResponse Stream(genomicsService service, StreamReadsRequest body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
// Make the request.
return(service.Reads.Stream(body).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Reads.Stream failed.", ex);
}
}
/// <summary>
/// Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together. If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally. For details on the requirements for each individual annotation resource, see CreateAnnotation.
/// Documentation https://developers.google.com/genomics/v1/reference/annotations/batchCreate
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <returns>BatchCreateAnnotationsResponseResponse</returns>
public static BatchCreateAnnotationsResponse BatchCreate(genomicsService service, BatchCreateAnnotationsRequest body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
// Make the request.
return(service.Annotations.BatchCreate(body).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Annotations.BatchCreate failed.", ex);
}
}
/// <summary>
/// Creates a new call set. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
/// Documentation https://developers.google.com/genomics/v1/reference/callsets/create
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="body">A valid genomics v1 body.</param>
/// <returns>CallSetResponse</returns>
public static CallSet Create(genomicsService service, CallSet body)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (body == null)
{
throw new ArgumentNullException("body");
}
// Make the request.
return(service.Callsets.Create(body).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Callsets.Create failed.", ex);
}
}
/// <summary>
/// Gets a call set by ID. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
/// Documentation https://developers.google.com/genomics/v1/reference/callsets/get
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="callSetId">The ID of the call set.</param>
/// <returns>CallSetResponse</returns>
public static CallSet Get(genomicsService service, string callSetId)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (callSetId == null)
{
throw new ArgumentNullException(callSetId);
}
// Make the request.
return(service.Callsets.Get(callSetId).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Callsets.Get failed.", ex);
}
}
/// <summary>
/// Deletes a pipeline based on ID. Caller must have WRITE permission to the project.
/// Documentation https://developers.google.com/genomics/v1alpha2/reference/pipelines/delete
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="pipelineId">Caller must have WRITE access to the project in which this pipeline is defined.</param>
/// <returns>EmptyResponse</returns>
public static Empty Delete(genomicsService service, string pipelineId)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
if (pipelineId == null)
{
throw new ArgumentNullException(pipelineId);
}
// Make the request.
return(service.Pipelines.Delete(pipelineId).Execute());
}
catch (Exception ex)
{
throw new Exception("Request Pipelines.Delete failed.", ex);
}
}
/// <summary>
/// Gets controller configuration information. Should only be called by VMs created by the Pipelines Service and not by end users.
/// Documentation https://developers.google.com/genomics/v1alpha2/reference/pipelines/getControllerConfig
/// Generation Note: This does not always build corectly. Google needs to standardise things I need to figuer out which ones are wrong.
/// </summary>
/// <param name="service">Authenticated genomics service.</param>
/// <param name="optional">Optional paramaters.</param> /// <returns>ControllerConfigResponse</returns>
public static ControllerConfig GetControllerConfig(genomicsService service, PipelinesGetControllerConfigOptionalParms optional = null)
{
try
{
// Initial validation.
if (service == null)
{
throw new ArgumentNullException("service");
}
// Building the initial request.
var request = service.Pipelines.GetControllerConfig();
// Applying optional parameters to the request.
request = (PipelinesResource.GetControllerConfigRequest)SampleHelpers.ApplyOptionalParms(request, optional);
// Requesting data.
return(request.Execute());
}
catch (Exception ex)
{
throw new Exception("Request Pipelines.GetControllerConfig failed.", ex);
}
}
