@aws-sdk/client-omics 3.331.0 → 3.335.0

package/dist-types/ts3.4/models/models_0.d.ts

@@ -2,6 +2,11 @@ import { ExceptionOptionType as __ExceptionOptionType } from "@aws-sdk/smithy-cl
 import { DocumentType as __DocumentType } from "@aws-sdk/types";
 import { Readable } from "stream";
 import { OmicsServiceException as __BaseException } from "./OmicsServiceException";
+export interface AbortMultipartReadSetUploadRequest {
+  sequenceStoreId: string | undefined;
+  uploadId: string | undefined;
+}
+export interface AbortMultipartReadSetUploadResponse {}
 export declare class AccessDeniedException extends __BaseException {
   readonly name: "AccessDeniedException";
   readonly $fault: "client";
@@ -9,6 +14,63 @@ export declare class AccessDeniedException extends __BaseException {
     opts: __ExceptionOptionType<AccessDeniedException, __BaseException>
   );
 }
+export declare class InternalServerException extends __BaseException {
+  readonly name: "InternalServerException";
+  readonly $fault: "server";
+  $retryable: {};
+  constructor(
+    opts: __ExceptionOptionType<InternalServerException, __BaseException>
+  );
+}
+export declare class NotSupportedOperationException extends __BaseException {
+  readonly name: "NotSupportedOperationException";
+  readonly $fault: "client";
+  constructor(
+    opts: __ExceptionOptionType<NotSupportedOperationException, __BaseException>
+  );
+}
+export declare class RequestTimeoutException extends __BaseException {
+  readonly name: "RequestTimeoutException";
+  readonly $fault: "client";
+  constructor(
+    opts: __ExceptionOptionType<RequestTimeoutException, __BaseException>
+  );
+}
+export declare class ResourceNotFoundException extends __BaseException {
+  readonly name: "ResourceNotFoundException";
+  readonly $fault: "client";
+  constructor(
+    opts: __ExceptionOptionType<ResourceNotFoundException, __BaseException>
+  );
+}
+export declare class ServiceQuotaExceededException extends __BaseException {
+  readonly name: "ServiceQuotaExceededException";
+  readonly $fault: "client";
+  constructor(
+    opts: __ExceptionOptionType<ServiceQuotaExceededException, __BaseException>
+  );
+}
+export declare class ThrottlingException extends __BaseException {
+  readonly name: "ThrottlingException";
+  readonly $fault: "client";
+  $retryable: {
+    throttling: boolean;
+  };
+  constructor(
+    opts: __ExceptionOptionType<ThrottlingException, __BaseException>
+  );
+}
+export declare class ValidationException extends __BaseException {
+  readonly name: "ValidationException";
+  readonly $fault: "client";
+  constructor(
+    opts: __ExceptionOptionType<ValidationException, __BaseException>
+  );
+}
+export declare const Accelerators: {
+  readonly GPU: "GPU";
+};
+export type Accelerators = (typeof Accelerators)[keyof typeof Accelerators];
 export declare const ReadSetActivationJobStatus: {
   readonly CANCELLED: "CANCELLED";
   readonly CANCELLING: "CANCELLING";
@@ -65,38 +127,6 @@ export interface CancelAnnotationImportRequest {
   jobId: string | undefined;
 }
 export interface CancelAnnotationImportResponse {}
-export declare class InternalServerException extends __BaseException {
-  readonly name: "InternalServerException";
-  readonly $fault: "server";
-  $retryable: {};
-  constructor(
-    opts: __ExceptionOptionType<InternalServerException, __BaseException>
-  );
-}
-export declare class ResourceNotFoundException extends __BaseException {
-  readonly name: "ResourceNotFoundException";
-  readonly $fault: "client";
-  constructor(
-    opts: __ExceptionOptionType<ResourceNotFoundException, __BaseException>
-  );
-}
-export declare class ThrottlingException extends __BaseException {
-  readonly name: "ThrottlingException";
-  readonly $fault: "client";
-  $retryable: {
-    throttling: boolean;
-  };
-  constructor(
-    opts: __ExceptionOptionType<ThrottlingException, __BaseException>
-  );
-}
-export declare class ValidationException extends __BaseException {
-  readonly name: "ValidationException";
-  readonly $fault: "client";
-  constructor(
-    opts: __ExceptionOptionType<ValidationException, __BaseException>
-  );
-}
 export interface GetAnnotationImportRequest {
   jobId: string | undefined;
 }
@@ -157,6 +187,7 @@ export interface GetAnnotationImportResponse {
   items: AnnotationImportItemDetail[] | undefined;
   runLeftNormalization: boolean | undefined;
   formatOptions: FormatOptions | undefined;
+  annotationFields?: Record<string, string>;
 }
 export interface ListAnnotationImportJobsFilter {
   status?: JobStatus | string;
@@ -177,24 +208,19 @@ export interface AnnotationImportJobItem {
   updateTime: Date | undefined;
   completionTime?: Date;
   runLeftNormalization?: boolean;
+  annotationFields?: Record<string, string>;
 }
 export interface ListAnnotationImportJobsResponse {
   annotationImportJobs?: AnnotationImportJobItem[];
   nextToken?: string;
 }
-export declare class ServiceQuotaExceededException extends __BaseException {
-  readonly name: "ServiceQuotaExceededException";
-  readonly $fault: "client";
-  constructor(
-    opts: __ExceptionOptionType<ServiceQuotaExceededException, __BaseException>
-  );
-}
 export interface StartAnnotationImportRequest {
   destinationName: string | undefined;
   roleArn: string | undefined;
   items: AnnotationImportItemSource[] | undefined;
   formatOptions?: FormatOptions;
   runLeftNormalization?: boolean;
+  annotationFields?: Record<string, string>;
 }
 export interface StartAnnotationImportResponse {
   jobId: string | undefined;
@@ -397,13 +423,6 @@ export interface ReadSetBatchError {
 export interface BatchDeleteReadSetResponse {
   errors?: ReadSetBatchError[];
 }
-export declare class RequestTimeoutException extends __BaseException {
-  readonly name: "RequestTimeoutException";
-  readonly $fault: "client";
-  constructor(
-    opts: __ExceptionOptionType<RequestTimeoutException, __BaseException>
-  );
-}
 export interface CancelRunRequest {
   id: string | undefined;
 }
@@ -411,6 +430,56 @@ export interface CancelVariantImportRequest {
   jobId: string | undefined;
 }
 export interface CancelVariantImportResponse {}
+export declare const ReadSetPartSource: {
+  readonly SOURCE1: "SOURCE1";
+  readonly SOURCE2: "SOURCE2";
+};
+export type ReadSetPartSource =
+  (typeof ReadSetPartSource)[keyof typeof ReadSetPartSource];
+export interface CompleteReadSetUploadPartListItem {
+  partNumber: number | undefined;
+  partSource: ReadSetPartSource | string | undefined;
+  checksum: string | undefined;
+}
+export interface CompleteMultipartReadSetUploadRequest {
+  sequenceStoreId: string | undefined;
+  uploadId: string | undefined;
+  parts: CompleteReadSetUploadPartListItem[] | undefined;
+}
+export interface CompleteMultipartReadSetUploadResponse {
+  readSetId: string | undefined;
+}
+export declare const FileType: {
+  readonly BAM: "BAM";
+  readonly CRAM: "CRAM";
+  readonly FASTQ: "FASTQ";
+};
+export type FileType = (typeof FileType)[keyof typeof FileType];
+export interface CreateMultipartReadSetUploadRequest {
+  sequenceStoreId: string | undefined;
+  clientToken?: string;
+  sourceFileType: FileType | string | undefined;
+  subjectId: string | undefined;
+  sampleId: string | undefined;
+  generatedFrom?: string;
+  referenceArn: string | undefined;
+  name: string | undefined;
+  description?: string;
+  tags?: Record<string, string>;
+}
+export interface CreateMultipartReadSetUploadResponse {
+  sequenceStoreId: string | undefined;
+  uploadId: string | undefined;
+  sourceFileType: FileType | string | undefined;
+  subjectId: string | undefined;
+  sampleId: string | undefined;
+  generatedFrom?: string;
+  referenceArn: string | undefined;
+  name?: string;
+  description?: string;
+  tags?: Record<string, string>;
+  creationTime: Date | undefined;
+}
 export interface CreateReferenceStoreRequest {
   name: string | undefined;
   description?: string;
@@ -433,6 +502,7 @@ export interface CreateRunGroupRequest {
   maxDuration?: number;
   tags?: Record<string, string>;
   requestId?: string;
+  maxGpus?: number;
 }
 export interface CreateRunGroupResponse {
   arn?: string;
@@ -445,6 +515,7 @@ export interface CreateSequenceStoreRequest {
   sseConfig?: SseConfig;
   tags?: Record<string, string>;
   clientToken?: string;
+  fallbackLocation?: string;
 }
 export interface CreateSequenceStoreResponse {
   id: string | undefined;
@@ -453,6 +524,7 @@ export interface CreateSequenceStoreResponse {
   description?: string;
   sseConfig?: SseConfig;
   creationTime: Date | undefined;
+  fallbackLocation?: string;
 }
 export interface CreateVariantStoreRequest {
   reference: ReferenceItem | undefined;
@@ -489,12 +561,14 @@ export interface CreateWorkflowRequest {
   storageCapacity?: number;
   tags?: Record<string, string>;
   requestId?: string;
+  accelerators?: Accelerators | string;
 }
 export declare const WorkflowStatus: {
   readonly ACTIVE: "ACTIVE";
   readonly CREATING: "CREATING";
   readonly DELETED: "DELETED";
   readonly FAILED: "FAILED";
+  readonly INACTIVE: "INACTIVE";
   readonly UPDATING: "UPDATING";
 };
 export type WorkflowStatus =
@@ -579,12 +653,6 @@ export interface FileInformation {
   partSize?: number;
   contentLength?: number;
 }
-export declare const FileType: {
-  readonly BAM: "BAM";
-  readonly CRAM: "CRAM";
-  readonly FASTQ: "FASTQ";
-};
-export type FileType = (typeof FileType)[keyof typeof FileType];
 export declare const ReadSetFile: {
   readonly INDEX: "INDEX";
   readonly SOURCE1: "SOURCE1";
@@ -706,6 +774,8 @@ export declare const ReadSetStatus: {
   readonly ARCHIVED: "ARCHIVED";
   readonly DELETED: "DELETED";
   readonly DELETING: "DELETING";
+  readonly PROCESSING_UPLOAD: "PROCESSING_UPLOAD";
+  readonly UPLOAD_FAILED: "UPLOAD_FAILED";
 };
 export type ReadSetStatus = (typeof ReadSetStatus)[keyof typeof ReadSetStatus];
 export interface GetReadSetMetadataResponse {
@@ -722,6 +792,7 @@ export interface GetReadSetMetadataResponse {
   sequenceInformation?: SequenceInformation;
   referenceArn?: string;
   files?: ReadSetFiles;
+  statusMessage?: string;
 }
 export declare const ReferenceFile: {
   readonly INDEX: "INDEX";
@@ -845,6 +916,7 @@ export declare const RunStatus: {
 export type RunStatus = (typeof RunStatus)[keyof typeof RunStatus];
 export declare const WorkflowType: {
   readonly PRIVATE: "PRIVATE";
+  readonly READY2RUN: "READY2RUN";
 };
 export type WorkflowType = (typeof WorkflowType)[keyof typeof WorkflowType];
 export interface GetRunResponse {
@@ -871,6 +943,7 @@ export interface GetRunResponse {
   stopTime?: Date;
   statusMessage?: string;
   tags?: Record<string, string>;
+  accelerators?: Accelerators | string;
 }
 export interface GetRunGroupRequest {
   id: string | undefined;
@@ -884,6 +957,7 @@ export interface GetRunGroupResponse {
   maxDuration?: number;
   creationTime?: Date;
   tags?: Record<string, string>;
+  maxGpus?: number;
 }
 export interface GetRunTaskRequest {
   id: string | undefined;
@@ -910,6 +984,7 @@ export interface GetRunTaskResponse {
   stopTime?: Date;
   statusMessage?: string;
   logStream?: string;
+  gpus?: number;
 }
 export interface GetSequenceStoreRequest {
   id: string | undefined;
@@ -921,6 +996,7 @@ export interface GetSequenceStoreResponse {
   description?: string;
   sseConfig?: SseConfig;
   creationTime: Date | undefined;
+  fallbackLocation?: string;
 }
 export interface GetVariantImportRequest {
   jobId: string | undefined;
@@ -941,6 +1017,7 @@ export interface GetVariantImportResponse {
   completionTime?: Date;
   items: VariantImportItemDetail[] | undefined;
   runLeftNormalization: boolean | undefined;
+  annotationFields?: Record<string, string>;
 }
 export interface GetVariantStoreRequest {
   name: string | undefined;
@@ -985,6 +1062,8 @@ export interface GetWorkflowResponse {
   creationTime?: Date;
   statusMessage?: string;
   tags?: Record<string, string>;
+  metadata?: Record<string, string>;
+  accelerators?: Accelerators | string;
 }
 export interface ImportReadSetFilter {
   status?: ReadSetImportJobStatus | string;
@@ -1012,6 +1091,28 @@ export interface ImportReferenceJobItem {
   creationTime: Date | undefined;
   completionTime?: Date;
 }
+export interface ListMultipartReadSetUploadsRequest {
+  sequenceStoreId: string | undefined;
+  maxResults?: number;
+  nextToken?: string;
+}
+export interface MultipartReadSetUploadListItem {
+  sequenceStoreId: string | undefined;
+  uploadId: string | undefined;
+  sourceFileType: FileType | string | undefined;
+  subjectId: string | undefined;
+  sampleId: string | undefined;
+  generatedFrom: string | undefined;
+  referenceArn: string | undefined;
+  name?: string;
+  description?: string;
+  tags?: Record<string, string>;
+  creationTime: Date | undefined;
+}
+export interface ListMultipartReadSetUploadsResponse {
+  nextToken?: string;
+  uploads?: MultipartReadSetUploadListItem[];
+}
 export interface ListReadSetActivationJobsRequest {
   sequenceStoreId: string | undefined;
   maxResults?: number;
@@ -1048,6 +1149,9 @@ export interface ReadSetFilter {
   referenceArn?: string;
   createdAfter?: Date;
   createdBefore?: Date;
+  sampleId?: string;
+  subjectId?: string;
+  generatedFrom?: string;
 }
 export interface ListReadSetsRequest {
   sequenceStoreId: string | undefined;
@@ -1068,11 +1172,36 @@ export interface ReadSetListItem {
   fileType: FileType | string | undefined;
   sequenceInformation?: SequenceInformation;
   creationTime: Date | undefined;
+  statusMessage?: string;
 }
 export interface ListReadSetsResponse {
   nextToken?: string;
   readSets: ReadSetListItem[] | undefined;
 }
+export interface ReadSetUploadPartListFilter {
+  createdAfter?: Date;
+  createdBefore?: Date;
+}
+export interface ListReadSetUploadPartsRequest {
+  sequenceStoreId: string | undefined;
+  uploadId: string | undefined;
+  partSource: ReadSetPartSource | string | undefined;
+  maxResults?: number;
+  nextToken?: string;
+  filter?: ReadSetUploadPartListFilter;
+}
+export interface ReadSetUploadPartListItem {
+  partNumber: number | undefined;
+  partSize: number | undefined;
+  partSource: ReadSetPartSource | string | undefined;
+  checksum: string | undefined;
+  creationTime?: Date;
+  lastUpdatedTime?: Date;
+}
+export interface ListReadSetUploadPartsResponse {
+  nextToken?: string;
+  parts?: ReadSetUploadPartListItem[];
+}
 export interface ListReferenceImportJobsRequest {
   maxResults?: number;
   nextToken?: string;
@@ -1145,6 +1274,7 @@ export interface RunGroupListItem {
   maxRuns?: number;
   maxDuration?: number;
   creationTime?: Date;
+  maxGpus?: number;
 }
 export interface ListRunGroupsResponse {
   items?: RunGroupListItem[];
@@ -1155,6 +1285,7 @@ export interface ListRunsRequest {
   runGroupId?: string;
   startingToken?: string;
   maxResults?: number;
+  status?: RunStatus | string;
 }
 export interface RunListItem {
   arn?: string;
@@ -1187,6 +1318,7 @@ export interface TaskListItem {
   creationTime?: Date;
   startTime?: Date;
   stopTime?: Date;
+  gpus?: number;
 }
 export interface ListRunTasksResponse {
   items?: TaskListItem[];
@@ -1209,6 +1341,7 @@ export interface SequenceStoreDetail {
   description?: string;
   sseConfig?: SseConfig;
   creationTime: Date | undefined;
+  fallbackLocation?: string;
 }
 export interface ListSequenceStoresResponse {
   nextToken?: string;
@@ -1239,6 +1372,7 @@ export interface VariantImportJobItem {
   updateTime: Date | undefined;
   completionTime?: Date;
   runLeftNormalization?: boolean;
+  annotationFields?: Record<string, string>;
 }
 export interface ListVariantImportJobsResponse {
   variantImportJobs?: VariantImportJobItem[];
@@ -1284,6 +1418,7 @@ export interface WorkflowListItem {
   type?: WorkflowType | string;
   digest?: string;
   creationTime?: Date;
+  metadata?: Record<string, string>;
 }
 export interface ListWorkflowsResponse {
   items?: WorkflowListItem[];
@@ -1314,6 +1449,7 @@ export interface UpdateRunGroupRequest {
   maxCpus?: number;
   maxRuns?: number;
   maxDuration?: number;
+  maxGpus?: number;
 }
 export interface StartRunRequest {
   workflowId?: string;
@@ -1388,6 +1524,16 @@ export interface StartReadSetImportJobResponse {
   status: ReadSetImportJobStatus | string | undefined;
   creationTime: Date | undefined;
 }
+export interface UploadReadSetPartRequest {
+  sequenceStoreId: string | undefined;
+  uploadId: string | undefined;
+  partSource: ReadSetPartSource | string | undefined;
+  partNumber: number | undefined;
+  payload: Readable | ReadableStream | Blob | undefined;
+}
+export interface UploadReadSetPartResponse {
+  checksum: string | undefined;
+}
 export interface TagResourceRequest {
   resourceArn: string | undefined;
   tags: Record<string, string> | undefined;
@@ -1406,6 +1552,7 @@ export interface StartVariantImportRequest {
   roleArn: string | undefined;
   items: VariantImportItemSource[] | undefined;
   runLeftNormalization?: boolean;
+  annotationFields?: Record<string, string>;
 }
 export interface StartVariantImportResponse {
   jobId: string | undefined;
@@ -1434,3 +1581,6 @@ export declare const GetReadSetResponseFilterSensitiveLog: (
 export declare const GetReferenceResponseFilterSensitiveLog: (
   obj: GetReferenceResponse
 ) => any;
+export declare const UploadReadSetPartRequestFilterSensitiveLog: (
+  obj: UploadReadSetPartRequest
+) => any;

package/dist-types/ts3.4/pagination/ListMultipartReadSetUploadsPaginator.d.ts

@@ -0,0 +1,11 @@
+import { Paginator } from "@aws-sdk/types";
+import {
+  ListMultipartReadSetUploadsCommandInput,
+  ListMultipartReadSetUploadsCommandOutput,
+} from "../commands/ListMultipartReadSetUploadsCommand";
+import { OmicsPaginationConfiguration } from "./Interfaces";
+export declare function paginateListMultipartReadSetUploads(
+  config: OmicsPaginationConfiguration,
+  input: ListMultipartReadSetUploadsCommandInput,
+  ...additionalArguments: any
+): Paginator<ListMultipartReadSetUploadsCommandOutput>;

package/dist-types/ts3.4/pagination/ListReadSetUploadPartsPaginator.d.ts

@@ -0,0 +1,11 @@
+import { Paginator } from "@aws-sdk/types";
+import {
+  ListReadSetUploadPartsCommandInput,
+  ListReadSetUploadPartsCommandOutput,
+} from "../commands/ListReadSetUploadPartsCommand";
+import { OmicsPaginationConfiguration } from "./Interfaces";
+export declare function paginateListReadSetUploadParts(
+  config: OmicsPaginationConfiguration,
+  input: ListReadSetUploadPartsCommandInput,
+  ...additionalArguments: any
+): Paginator<ListReadSetUploadPartsCommandOutput>;

package/dist-types/ts3.4/pagination/index.d.ts

@@ -1,9 +1,11 @@
 export * from "./Interfaces";
 export * from "./ListAnnotationImportJobsPaginator";
 export * from "./ListAnnotationStoresPaginator";
+export * from "./ListMultipartReadSetUploadsPaginator";
 export * from "./ListReadSetActivationJobsPaginator";
 export * from "./ListReadSetExportJobsPaginator";
 export * from "./ListReadSetImportJobsPaginator";
+export * from "./ListReadSetUploadPartsPaginator";
 export * from "./ListReadSetsPaginator";
 export * from "./ListReferenceImportJobsPaginator";
 export * from "./ListReferenceStoresPaginator";