{ "openapi": "3.1.0", "info": { "title": "Element Biosciences Cloud API", "description": "The Element Biosciences Cloud API provides programmatic access to data in\nthe Element Biosciences Cloud platform: instrument runs (sequencing and\nmultiomics), workflow executions, registered instruments, storage\nconnections, and the files those resources produce.\n\nAll paths are versioned under `/v1`.\n\n## Authentication\nEvery request must include an API key in the `x-api-key` header. Create and\nmanage keys in the Element Biosciences Cloud console. Call `GET /v1/auth` to\nconfirm which tenant a key belongs to.\n\n## Scopes\nEach API key carries one or more scopes of the form\n`resource:action[:resource_id]`, for example `runs:read`,\n`executions:download`, or `storage:download:{connection_id}`. A request that\nis authenticated but lacks the required scope fails with HTTP 403 and the\n`INSUFFICIENT_SCOPE` reason. List endpoints transparently restrict results\nto the resources a key is scoped to.\n\n## Pagination\nList endpoints are cursor-paginated. Set `page_size` to control the page\nlength and pass the `next_page_token` from one response as the `page_token`\nof the next; an empty `next_page_token` indicates the last page.\n\n## Errors\nErrors return a JSON body with an integer `code`, a human-readable\n`message`, and a `details` array. Each detail carries a machine-readable\n`reason` (for example `RUN_NOT_FOUND` or `INVALID_API_KEY`) and the\n`domain` `cloud-api.elembio.io`. The `request_id` in the detail metadata\nmatches the `X-Request-ID` response header; include it when reporting\nproblems.\n", "version": "1.0.0", "contact": { "name": "Element Biosciences", "url": "https://www.elembio.io" } }, "servers": [ { "url": "https://cloud-api.usw2.elembio.io", "description": "Production" } ], "security": [ { "apiKey": [] } ], "components": { "securitySchemes": { "apiKey": { "type": "apiKey", "in": "header", "name": "x-api-key", "description": "API key obtained from the Element Biosciences Cloud console" } }, "schemas": { "Error": { "type": "object", "description": "Error response returned by all endpoints when a request fails.", "properties": { "code": { "type": "integer", "description": "Numeric status code corresponding to the HTTP response status" }, "message": { "type": "string", "description": "Human-readable error message" }, "details": { "type": "array", "description": "Structured error details with machine-readable reason codes", "items": { "$ref": "#/components/schemas/ErrorDetail" } } }, "required": [ "code", "message" ], "examples": [ { "code": 404, "message": "Run not found.", "details": [ { "reason": "RUN_NOT_FOUND", "domain": "cloud-api.elembio.io", "metadata": { "request_id": "550e8400-e29b-41d4-a716-446655440000" } } ] }, { "code": 401, "message": "Invalid API key.", "details": [ { "reason": "INVALID_API_KEY", "domain": "cloud-api.elembio.io", "metadata": { "request_id": "550e8400-e29b-41d4-a716-446655440001" } } ] } ] }, "ErrorDetail": { "type": "object", "description": "Structured error detail with a machine-readable reason code.", "properties": { "@type": { "type": "string", "description": "Type identifier for this error detail" }, "reason": { "type": "string", "description": "Machine-readable error code identifying the specific failure\n(e.g. RUN_NOT_FOUND, INVALID_API_KEY, INSUFFICIENT_SCOPE).\n", "examples": [ "RUN_NOT_FOUND", "INVALID_API_KEY", "MISSING_API_KEY", "INSUFFICIENT_SCOPE", "INTERNAL_ERROR" ] }, "domain": { "type": "string", "description": "Identifies the system that generated the error", "const": "cloud-api.elembio.io" }, "metadata": { "type": "object", "description": "Additional context for the error", "properties": { "request_id": { "type": "string", "description": "Request ID matching the X-Request-ID response header" } } } }, "required": [ "reason", "domain" ] }, "elembio.cloud.v1.Batch": { "type": "object", "properties": { "name": { "type": "string", "title": "name" }, "cycles": { "type": "integer", "title": "cycles", "format": "int32" }, "order": { "type": "integer", "title": "order", "format": "int32" } }, "title": "Batch", "additionalProperties": false, "description": "Batch information for multiomics runs" }, "elembio.cloud.v1.Cartridge": { "type": "object", "properties": { "id": { "type": "string", "title": "id" }, "name": { "type": "string", "title": "name" }, "partNumber": { "type": "string", "title": "part_number" } }, "title": "Cartridge", "additionalProperties": false, "description": "Cartridge information for multiomics runs" }, "elembio.cloud.v1.Consumable": { "type": "object", "properties": { "serialNumber": { "type": "string", "title": "serial_number" }, "partNumber": { "type": "string", "title": "part_number" }, "lotNumber": { "type": "string", "title": "lot_number" }, "expiration": { "title": "expiration", "$ref": "#/components/schemas/google.protobuf.Timestamp" } }, "title": "Consumable", "additionalProperties": false, "description": "Consumable information (used for both run types)" }, "elembio.cloud.v1.Execution": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "Unique identifier for the execution" }, "name": { "type": "string", "title": "name", "description": "Human-readable name of the execution" }, "status": { "title": "status", "description": "Current status of the execution", "$ref": "#/components/schemas/elembio.cloud.v1.ExecutionStatus" }, "statusDescription": { "type": "string", "title": "status_description", "description": "Detailed status description from the compute platform" }, "platform": { "type": "string", "title": "platform", "description": "Compute platform running this execution.\n Possible values: \"aws_omics\", \"seqera\", \"dnanexus\", \"catalyst\"." }, "workflow": { "title": "workflow", "description": "Workflow information", "$ref": "#/components/schemas/elembio.cloud.v1.Workflow" }, "flow": { "title": "flow", "description": "Flow (configured workflow) used for this execution", "$ref": "#/components/schemas/elembio.cloud.v1.Flow" }, "inputs": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.ExecutionInput" }, "title": "inputs", "description": "Input data sources" }, "output": { "title": "output", "description": "Output location and content types", "$ref": "#/components/schemas/elembio.cloud.v1.Output" }, "startedBy": { "title": "started_by", "description": "User who started the execution", "$ref": "#/components/schemas/elembio.cloud.v1.UserSummary" }, "timeCreated": { "title": "time_created", "description": "Timestamps", "$ref": "#/components/schemas/google.protobuf.Timestamp" }, "timeStarted": { "oneOf": [ { "$ref": "#/components/schemas/google.protobuf.Timestamp" }, { "type": "null" } ], "title": "time_started" }, "timeCompleted": { "oneOf": [ { "$ref": "#/components/schemas/google.protobuf.Timestamp" }, { "type": "null" } ], "title": "time_completed" }, "errorMessage": { "type": [ "string", "null" ], "title": "error_message", "description": "Human-readable error summary describing why the execution failed.\n Use GetExecutionLogs for full provider error and log output." } }, "title": "Execution", "additionalProperties": false, "description": "An Execution represents a workflow run processing instrument data" }, "elembio.cloud.v1.ExecutionInput": { "type": "object", "oneOf": [ { "type": "object", "properties": { "execution": { "title": "execution", "description": "Upstream execution reference", "$ref": "#/components/schemas/elembio.cloud.v1.ExecutionReference" } }, "title": "execution", "required": [ "execution" ] }, { "type": "object", "properties": { "run": { "title": "run", "description": "Instrument run reference", "$ref": "#/components/schemas/elembio.cloud.v1.RunReference" } }, "title": "run", "required": [ "run" ] } ], "title": "ExecutionInput", "description": "Input data source for the execution" }, "elembio.cloud.v1.ExecutionReference": { "type": "object", "properties": { "id": { "type": "string", "title": "id" }, "name": { "type": "string", "title": "name" }, "workflowName": { "type": "string", "title": "workflow_name" } }, "title": "ExecutionReference", "additionalProperties": false, "description": "Reference to an upstream execution" }, "elembio.cloud.v1.ExecutionStatus": { "type": "string", "title": "ExecutionStatus", "enum": [ "EXECUTION_STATUS_UNSPECIFIED", "EXECUTION_STATUS_INITIALIZED", "EXECUTION_STATUS_UNTRIGGERED", "EXECUTION_STATUS_PENDING", "EXECUTION_STATUS_RUNNING", "EXECUTION_STATUS_COMPLETED", "EXECUTION_STATUS_FAILED", "EXECUTION_STATUS_CANCELED" ], "description": "Execution status" }, "elembio.cloud.v1.File": { "type": "object", "properties": { "path": { "type": "string", "title": "path", "description": "Path within the namespace of the RPC that returned this file.\n Namespace is the run / execution / storage connection, depending on\n the RPC. Round-trips with the request prefix: paste any returned\n path back into a subsequent --prefix to drill in.\n Example: \"A24-S2/run-001/manifest.json\"." }, "name": { "type": "string", "title": "name", "description": "Filename portion of the path (convenience field)\n Example: \"sample1.fastq.gz\"" }, "size": { "type": [ "integer", "string" ], "title": "size", "format": "int64", "description": "Size in bytes" }, "lastModified": { "title": "last_modified", "description": "Last modification timestamp", "$ref": "#/components/schemas/google.protobuf.Timestamp" }, "uri": { "type": "string", "title": "uri", "description": "Full URI for the object — always storage-absolute, regardless of the\n RPC. Use this for direct backend access (S3 SDK, etc.).\n Example: \"s3://bucket-name/runs/run-123/outputs/sample1.fastq.gz\"" }, "downloadUrl": { "type": "string", "title": "download_url", "description": "Pre-signed URL for downloading this object over HTTP GET.\n Populated only when the request set include_download_url = true; empty\n otherwise. The URL is a short-lived credential — fetch promptly and do\n not persist it. For bulk or repeated downloads, request download\n credentials instead." }, "storageClass": { "type": [ "string", "null" ], "title": "storage_class", "description": "Storage class of the object. Examples: \"STANDARD\", \"GLACIER\",\n \"DEEP_ARCHIVE\"." } }, "title": "File", "additionalProperties": false, "description": "A File represents an object in cloud storage." }, "elembio.cloud.v1.Flow": { "type": "object", "properties": { "id": { "type": "string", "title": "id" }, "name": { "type": "string", "title": "name" } }, "title": "Flow", "additionalProperties": false, "description": "Flow represents a configured workflow" }, "elembio.cloud.v1.GetAuthRequest": { "type": "object", "title": "GetAuthRequest", "additionalProperties": false, "description": "Request for authentication information. Empty: the API key is read from the\n x-api-key request header." }, "elembio.cloud.v1.GetAuthResponse": { "type": "object", "properties": { "tenantId": { "type": "string", "title": "tenant_id", "description": "Identifier of the tenant the API key belongs to." }, "scopes": { "type": "array", "items": { "type": "string" }, "title": "scopes", "description": "Scopes granted to the API key making the request, e.g. \"runs:read\" or\n \"storage:download:stc_abc123/data/\". A resource-scoped key reports its\n resource-qualified scopes; an unrestricted key reports its family-level\n scopes. An empty list means the key has no resource scopes (only the\n auth-level access needed to reach this endpoint)." } }, "title": "GetAuthResponse", "additionalProperties": false, "description": "Response describing the authenticated API key." }, "elembio.cloud.v1.GetDownloadCredentialsRequest": { "type": "object", "properties": { "storageConnectionId": { "type": "string", "title": "storage_connection_id", "description": "The storage connection ID" }, "prefix": { "type": [ "string", "null" ], "title": "prefix", "description": "Prefix to scope credentials to a subdirectory, relative to the storage\n connection's configured root. Matches the --prefix semantics of ListFiles:\n optional for an unrestricted key (omitted ⇒ connection root), but required\n and bounded to scope for a key scoped to a path prefix — omitting it or\n naming one outside the scope returns PermissionDenied with the allowed\n prefix(es) (`allowed_prefixes` metadata)." }, "expirationSeconds": { "type": [ "integer", "null" ], "title": "expiration_seconds", "format": "int32", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected." } }, "title": "GetDownloadCredentialsRequest", "required": [ "storageConnectionId" ], "additionalProperties": false, "description": "Request to get temporary download credentials for a storage connection" }, "elembio.cloud.v1.GetDownloadCredentialsResponse": { "type": "object", "oneOf": [ { "type": "object", "properties": { "s3": { "title": "s3", "$ref": "#/components/schemas/elembio.cloud.v1.S3Credentials" } }, "title": "s3", "required": [ "s3" ] } ], "title": "GetDownloadCredentialsResponse", "description": "Response containing temporary download credentials" }, "elembio.cloud.v1.GetExecutionDownloadCredentialsRequest": { "type": "object", "properties": { "executionId": { "type": "string", "title": "execution_id", "description": "The execution ID" }, "prefix": { "type": [ "string", "null" ], "title": "prefix", "description": "Optional path prefix within the execution to scope credentials to.\n Execution-relative, identical semantics to\n ListExecutionFilesRequest.prefix. \"..\" segments are rejected.\n When omitted, credentials are scoped to the whole execution (the\n execution root)." }, "expirationSeconds": { "type": [ "integer", "null" ], "title": "expiration_seconds", "format": "int32", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected." } }, "title": "GetExecutionDownloadCredentialsRequest", "required": [ "executionId" ], "additionalProperties": false, "description": "Request to get temporary download credentials for an execution" }, "elembio.cloud.v1.GetExecutionDownloadCredentialsResponse": { "type": "object", "oneOf": [ { "type": "object", "properties": { "s3": { "title": "s3", "$ref": "#/components/schemas/elembio.cloud.v1.S3Credentials" } }, "title": "s3", "required": [ "s3" ] } ], "title": "GetExecutionDownloadCredentialsResponse", "description": "Response containing temporary download credentials for an execution" }, "elembio.cloud.v1.GetExecutionLogsRequest": { "type": "object", "properties": { "executionId": { "type": "string", "title": "execution_id", "description": "The execution ID" } }, "title": "GetExecutionLogsRequest", "required": [ "executionId" ], "additionalProperties": false, "description": "Request to get logs for an execution" }, "elembio.cloud.v1.GetExecutionLogsResponse": { "type": "object", "properties": { "error": { "type": "string", "title": "error", "description": "Error output from the compute platform (if any)" }, "log": { "type": "string", "title": "log", "description": "Full execution log from the compute platform (if any)" } }, "title": "GetExecutionLogsResponse", "additionalProperties": false, "description": "Response containing execution logs" }, "elembio.cloud.v1.GetExecutionRequest": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "The unique identifier of the execution" } }, "title": "GetExecutionRequest", "required": [ "id" ], "additionalProperties": false, "description": "Request to get a specific execution" }, "elembio.cloud.v1.GetExecutionResponse": { "type": "object", "properties": { "execution": { "title": "execution", "$ref": "#/components/schemas/elembio.cloud.v1.Execution" } }, "title": "GetExecutionResponse", "additionalProperties": false, "description": "Response containing a single execution with full details" }, "elembio.cloud.v1.GetInstrumentRequest": { "type": "object", "properties": { "serialNumber": { "type": "string", "title": "serial_number", "description": "Serial number of the instrument to retrieve. Example: \"AV223501\"." } }, "title": "GetInstrumentRequest", "required": [ "serialNumber" ], "additionalProperties": false, "description": "Request to get a single instrument." }, "elembio.cloud.v1.GetInstrumentResponse": { "type": "object", "properties": { "instrument": { "title": "instrument", "$ref": "#/components/schemas/elembio.cloud.v1.Instrument" } }, "title": "GetInstrumentResponse", "additionalProperties": false, "description": "Response containing a single instrument." }, "elembio.cloud.v1.GetRunDownloadCredentialsRequest": { "type": "object", "properties": { "runId": { "type": "string", "title": "run_id", "description": "The run ID" }, "prefix": { "type": [ "string", "null" ], "title": "prefix", "description": "Optional path prefix within the run to scope credentials to.\n Run-relative, identical semantics to ListRunFilesRequest.prefix.\n \"..\" segments are rejected. When omitted, credentials are scoped to\n the whole run (the run root)." }, "expirationSeconds": { "type": [ "integer", "null" ], "title": "expiration_seconds", "format": "int32", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected." } }, "title": "GetRunDownloadCredentialsRequest", "required": [ "runId" ], "additionalProperties": false, "description": "Request to get temporary download credentials for a run" }, "elembio.cloud.v1.GetRunDownloadCredentialsResponse": { "type": "object", "oneOf": [ { "type": "object", "properties": { "s3": { "title": "s3", "$ref": "#/components/schemas/elembio.cloud.v1.S3Credentials" } }, "title": "s3", "required": [ "s3" ] } ], "title": "GetRunDownloadCredentialsResponse", "description": "Response containing temporary download credentials for a run" }, "elembio.cloud.v1.GetRunRequest": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "The unique identifier of the run" } }, "title": "GetRunRequest", "required": [ "id" ], "additionalProperties": false, "description": "Request to get a specific run" }, "elembio.cloud.v1.GetRunResponse": { "type": "object", "properties": { "run": { "title": "run", "$ref": "#/components/schemas/elembio.cloud.v1.Run" } }, "title": "GetRunResponse", "additionalProperties": false, "description": "Response containing a single run with full details" }, "elembio.cloud.v1.GetStorageConnectionRequest": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "ID of the storage connection to retrieve." } }, "title": "GetStorageConnectionRequest", "required": [ "id" ], "additionalProperties": false, "description": "Request to get a single storage connection." }, "elembio.cloud.v1.GetStorageConnectionResponse": { "type": "object", "properties": { "storageConnection": { "title": "storage_connection", "$ref": "#/components/schemas/elembio.cloud.v1.StorageConnection" } }, "title": "GetStorageConnectionResponse", "additionalProperties": false, "description": "Response containing a single storage connection" }, "elembio.cloud.v1.Instrument": { "type": "object", "properties": { "serialNumber": { "type": "string", "title": "serial_number", "description": "Serial number that uniquely identifies the instrument. Example: \"AV223501\"." }, "name": { "type": "string", "title": "name", "description": "Human-readable name assigned to the instrument, if any." }, "model": { "type": "string", "title": "model", "description": "Instrument model. Possible values: \"AVITI\", \"VITARI\". Empty when the\n model is unknown." }, "status": { "title": "status", "description": "Current operational status of the instrument.", "$ref": "#/components/schemas/elembio.cloud.v1.InstrumentStatus" }, "timeCreated": { "title": "time_created", "description": "When the instrument was first registered.", "$ref": "#/components/schemas/google.protobuf.Timestamp" }, "timeUpdated": { "title": "time_updated", "description": "When the instrument record was last updated.", "$ref": "#/components/schemas/google.protobuf.Timestamp" }, "timeLastConnected": { "oneOf": [ { "$ref": "#/components/schemas/google.protobuf.Timestamp" }, { "type": "null" } ], "title": "time_last_connected", "description": "When the instrument was last connected to the cloud, if known." }, "softwareVersion": { "type": [ "string", "null" ], "title": "software_version", "description": "Software version currently installed on the instrument (AOS version)." } }, "title": "Instrument", "additionalProperties": false, "description": "An Instrument represents a registered sequencing or multiomics device." }, "elembio.cloud.v1.InstrumentStatus": { "type": "string", "title": "InstrumentStatus", "enum": [ "INSTRUMENT_STATUS_UNSPECIFIED", "INSTRUMENT_STATUS_ACTIVE", "INSTRUMENT_STATUS_INACTIVE", "INSTRUMENT_STATUS_DECOMMISSIONED" ], "description": "Status of an instrument." }, "elembio.cloud.v1.ListExecutionFilesRequest": { "type": "object", "properties": { "executionId": { "type": "string", "title": "execution_id", "description": "The execution ID" }, "prefix": { "type": [ "string", "null" ], "title": "prefix", "description": "Path prefix within the execution, e.g. \"visualization/\" or \"Stats/foo\".\n The execution is a self-contained namespace: paths do not include any\n bucket-level or workflow-level layout. Round-trips with File.path\n returned by this RPC. \"..\" segments are rejected.\n Optional: when omitted, lists the whole execution (the execution root)." }, "recursive": { "type": [ "boolean", "null" ], "title": "recursive", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level" }, "pageSize": { "type": [ "integer", "null" ], "title": "page_size", "format": "int32", "description": "Maximum number of files to return per page (default: 1000, max: 1000)" }, "pageToken": { "type": [ "string", "null" ], "title": "page_token", "description": "Continuation token from previous response (passthrough from storage)" }, "includeDownloadUrl": { "type": [ "boolean", "null" ], "title": "include_download_url", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetExecutionDownloadCredentials when\n long-lived bulk access is required." }, "downloadUrlExpirationSeconds": { "type": [ "integer", "null" ], "title": "download_url_expiration_seconds", "format": "int32", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days." }, "includeDownloadChecksum": { "type": [ "boolean", "null" ], "title": "include_download_checksum", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field." } }, "title": "ListExecutionFilesRequest", "required": [ "executionId" ], "additionalProperties": false, "description": "Request to list files for an execution" }, "elembio.cloud.v1.ListExecutionFilesResponse": { "type": "object", "properties": { "files": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.File" }, "title": "files", "description": "List of files" }, "subdirectories": { "type": "array", "items": { "type": "string" }, "title": "subdirectories", "description": "Subdirectories at this level (only populated when recursive=false)" }, "nextPageToken": { "type": "string", "title": "next_page_token", "description": "Continuation token for the next page" }, "isTruncated": { "type": "boolean", "title": "is_truncated", "description": "Indicates if the results were truncated" } }, "title": "ListExecutionFilesResponse", "additionalProperties": false, "description": "Response containing files for an execution" }, "elembio.cloud.v1.ListExecutionsRequest": { "type": "object", "properties": { "filter": { "type": [ "string", "null" ], "title": "filter", "description": "Search and filter expression. Space-separated `keyword:value` terms are\n ANDed together; bare text with no keyword searches all string fields. For\n date fields, replace the colon with a comparison operator (`>=`, `<=`,\n `>`, `<`, `!=`). List alternatives for one keyword with commas, e.g.\n `status:running,pending`. Dates accept ISO-8601 or relative offsets such\n as `24h`, `7d`, or `1mo`.\n\n Filterable keywords:\n\n - **String:** `name`, `input.run.id`, `input.run.name`, `input.run.instrument_name`, `input.execution.id`, `input.execution.name`, `flow.name`, `workflow.name`, `started_by`\n - **Enum:** `status`, `platform` (`aws_omics`, `seqera`, `dnanexus`, `catalyst`), `output.kind` (`fastq`, `bam`, `vcf`, `cram`, `parquet`)\n - **Date:** `time_created`, `time_started`, `time_completed`, `time_updated`\n\n Examples:\n\n - `workflow.name:bases2fastq status:running`\n - `platform:seqera output.kind:fastq time_completed>=24h`" }, "pageSize": { "type": [ "integer", "null" ], "title": "page_size", "format": "int32", "description": "Maximum number of executions to return (default: 100, max: 1000)" }, "pageToken": { "type": [ "string", "null" ], "title": "page_token", "description": "Token for pagination" }, "includeTotalCount": { "type": [ "boolean", "null" ], "title": "include_total_count", "description": "If true, include total_count in the response (adds a count query)" } }, "title": "ListExecutionsRequest", "additionalProperties": false, "description": "Request to list executions" }, "elembio.cloud.v1.ListExecutionsResponse": { "type": "object", "properties": { "executions": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.Execution" }, "title": "executions", "description": "List of executions" }, "nextPageToken": { "type": "string", "title": "next_page_token", "description": "Token for the next page (empty if no more results)" }, "previousPageToken": { "type": "string", "title": "previous_page_token", "description": "Token for the previous page (empty if on first page)" }, "totalCount": { "type": [ "integer", "null" ], "title": "total_count", "format": "int32", "description": "Total number of executions matching the filter (only if include_total_count was true)" } }, "title": "ListExecutionsResponse", "additionalProperties": false, "description": "Response containing a list of executions" }, "elembio.cloud.v1.ListFilesRequest": { "type": "object", "properties": { "storageConnectionId": { "type": "string", "title": "storage_connection_id", "description": "The storage connection ID to browse" }, "prefix": { "type": [ "string", "null" ], "title": "prefix", "description": "Path prefix relative to the storage connection's configured root,\n directory-shape with implicit trailing \"/\". The connection's saved\n sub-prefix (if any) is not part of this value — it's an\n implementation detail of the connection.\n Example: \"A24-S2/run-001/\". Round-trips with File.path.\n For an unrestricted key, optional: omitting it lists from the connection\n root. For a key scoped to a path prefix, a prefix WITHIN the scope is\n required: omitting it, or supplying one outside the scope, returns\n PermissionDenied with the allowed prefix(es) in the error\n (`allowed_prefixes` metadata)." }, "recursive": { "type": [ "boolean", "null" ], "title": "recursive", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level" }, "pageSize": { "type": [ "integer", "null" ], "title": "page_size", "format": "int32", "description": "Maximum number of files to return per page (default: 1000, max: 1000)\n Note: This is passed through to the underlying storage system" }, "pageToken": { "type": [ "string", "null" ], "title": "page_token", "description": "Continuation token from previous response\n This is an opaque token from the underlying storage system" }, "includeDownloadUrl": { "type": [ "boolean", "null" ], "title": "include_download_url", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetDownloadCredentials when long-lived bulk\n access is required." }, "downloadUrlExpirationSeconds": { "type": [ "integer", "null" ], "title": "download_url_expiration_seconds", "format": "int32", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days." }, "includeDownloadChecksum": { "type": [ "boolean", "null" ], "title": "include_download_checksum", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field." } }, "title": "ListFilesRequest", "required": [ "storageConnectionId" ], "additionalProperties": false, "description": "Request to list files in a storage connection" }, "elembio.cloud.v1.ListFilesResponse": { "type": "object", "properties": { "files": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.File" }, "title": "files", "description": "List of files matching the request" }, "subdirectories": { "type": "array", "items": { "type": "string" }, "title": "subdirectories", "description": "Subdirectories at this level (only populated when recursive=false).\n Namespace-relative, matching the request prefix.\n Example: [\"A24-S2/\", \"A24-S2_other/\"]" }, "nextPageToken": { "type": "string", "title": "next_page_token", "description": "Continuation token for the next page (empty if no more results)\n This is an opaque token from the underlying storage system" }, "isTruncated": { "type": "boolean", "title": "is_truncated", "description": "Indicates if the results were truncated (more results available)" } }, "title": "ListFilesResponse", "additionalProperties": false, "description": "Response containing files and pagination info" }, "elembio.cloud.v1.ListInstrumentsRequest": { "type": "object", "properties": { "pageSize": { "type": [ "integer", "null" ], "title": "page_size", "format": "int32", "description": "Maximum number of instruments to return. Defaults to 100; values above\n 1000 are capped at 1000." }, "pageToken": { "type": [ "string", "null" ], "title": "page_token", "description": "Pagination token from a previous response's next_page_token. Omit to\n request the first page." } }, "title": "ListInstrumentsRequest", "additionalProperties": false, "description": "Request to list instruments." }, "elembio.cloud.v1.ListInstrumentsResponse": { "type": "object", "properties": { "instruments": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.Instrument" }, "title": "instruments", "description": "The instruments on this page." }, "nextPageToken": { "type": "string", "title": "next_page_token", "description": "Token for the next page, or empty when there are no more results." } }, "title": "ListInstrumentsResponse", "additionalProperties": false, "description": "Response containing a page of instruments." }, "elembio.cloud.v1.ListRunFilesRequest": { "type": "object", "properties": { "runId": { "type": "string", "title": "run_id", "description": "The run ID" }, "prefix": { "type": [ "string", "null" ], "title": "prefix", "description": "Path prefix within the run, e.g. \"visualization/\" or \"Stats/foo\".\n The run is a self-contained namespace: paths do not include any\n bucket-level or workflow-level layout. Round-trips with File.path\n returned by this RPC. \"..\" segments are rejected.\n Optional: when omitted, lists the whole run (the run root)." }, "recursive": { "type": [ "boolean", "null" ], "title": "recursive", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level" }, "pageSize": { "type": [ "integer", "null" ], "title": "page_size", "format": "int32", "description": "Maximum number of files to return per page (default: 1000, max: 1000)" }, "pageToken": { "type": [ "string", "null" ], "title": "page_token", "description": "Continuation token from previous response (passthrough from storage)" }, "includeDownloadUrl": { "type": [ "boolean", "null" ], "title": "include_download_url", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetRunDownloadCredentials when long-lived\n bulk access is required." }, "downloadUrlExpirationSeconds": { "type": [ "integer", "null" ], "title": "download_url_expiration_seconds", "format": "int32", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days." }, "includeDownloadChecksum": { "type": [ "boolean", "null" ], "title": "include_download_checksum", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field." } }, "title": "ListRunFilesRequest", "required": [ "runId" ], "additionalProperties": false, "description": "Request to list files for a run" }, "elembio.cloud.v1.ListRunFilesResponse": { "type": "object", "properties": { "files": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.File" }, "title": "files", "description": "List of files" }, "subdirectories": { "type": "array", "items": { "type": "string" }, "title": "subdirectories", "description": "Subdirectories at this level (only populated when recursive=false)" }, "nextPageToken": { "type": "string", "title": "next_page_token", "description": "Continuation token for the next page" }, "isTruncated": { "type": "boolean", "title": "is_truncated", "description": "Indicates if the results were truncated" } }, "title": "ListRunFilesResponse", "additionalProperties": false, "description": "Response containing files for a run" }, "elembio.cloud.v1.ListRunsRequest": { "type": "object", "properties": { "filter": { "type": [ "string", "null" ], "title": "filter", "description": "Search and filter expression. Space-separated `keyword:value` terms are\n ANDed together; bare text with no keyword searches all string fields. For\n numeric and date fields, replace the colon with a comparison operator\n (`>=`, `<=`, `>`, `<`, `!=`). List alternatives for one keyword with\n commas, e.g. `status:completed,failed`. Dates accept ISO-8601 or relative\n offsets such as `7d` or `1mo`.\n\n Filterable keywords:\n\n - **String:** `name`, `id`, `description`, `tags`, `instrument.name`, `instrument.serial_number`, `instrument.model`, `storage.connection_id`, `setup.sequencing.kit_name`, `setup.sequencing.library_structure`, `setup.sequencing.prep_type`, `setup.sequencing.polony_density`, `setup.sequencing.filter_mask`, `setup.sequencing.panel.name`, `setup.multiomics.panel.name`, `setup.multiomics.cartridge.name`\n - **Enum:** `type` (`sequencing`, `multiomics`), `status`, `output.kind` (`sequencing_run`, `multiomics_run`; an alias for `type`), `setup.multiomics.kit_type` (`cytoprofiling`, `direct_in_sample_sequencing`, `antibody_screening`, `tissue`, `protein_screening`), `setup.multiomics.well_layout` (`twelve_well_circle`, `twelve_well_square`, `two_well`, `one_well`, `twelve_well_standard`, `forty_eight_well`)\n - **Date:** `time_created`, `time_started`, `time_completed`, `time_updated`\n - **Numeric:** `metrics.sequencing.total_reads`, `metrics.sequencing.total_yield`, `metrics.sequencing.estimated_reads`, `metrics.sequencing.q30`, `metrics.sequencing.q40`, `metrics.sequencing.q50`, `metrics.sequencing.avg_q`, `metrics.sequencing.error_rate`, `metrics.sequencing.phix_alignment_rate`, `metrics.multiomics.total_cell_count`, `metrics.multiomics.total_cell_confluency`, `metrics.multiomics.total_percent_assigned`, `setup.sequencing.pmg_shift`\n - **Boolean:** `setup.sequencing.low_diversity`\n\n Examples:\n\n - `type:sequencing status:completed time_completed>=7d`\n - `instrument.serial_number:AV223501 metrics.sequencing.q30>=90`" }, "pageSize": { "type": [ "integer", "null" ], "title": "page_size", "format": "int32", "description": "Maximum number of runs to return (default: 100, max: 1000)" }, "pageToken": { "type": [ "string", "null" ], "title": "page_token", "description": "Token for pagination" }, "includeTotalCount": { "type": [ "boolean", "null" ], "title": "include_total_count", "description": "If true, include total_count in the response (adds a count query)" } }, "title": "ListRunsRequest", "additionalProperties": false, "description": "Request to list runs" }, "elembio.cloud.v1.ListRunsResponse": { "type": "object", "properties": { "runs": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.Run" }, "title": "runs", "description": "List of runs" }, "nextPageToken": { "type": "string", "title": "next_page_token", "description": "Token for the next page (empty if no more results)" }, "previousPageToken": { "type": "string", "title": "previous_page_token", "description": "Token for the previous page (empty if on first page)" }, "totalCount": { "type": [ "integer", "null" ], "title": "total_count", "format": "int32", "description": "Total number of runs matching the filter (only if include_total_count was true)" } }, "title": "ListRunsResponse", "additionalProperties": false, "description": "Response containing a list of runs" }, "elembio.cloud.v1.ListStorageConnectionsRequest": { "type": "object", "properties": { "pageSize": { "type": [ "integer", "null" ], "title": "page_size", "format": "int32", "description": "Maximum number of connections to return. Defaults to 100; values above\n 1000 are capped at 1000." }, "pageToken": { "type": [ "string", "null" ], "title": "page_token", "description": "Pagination token from a previous response's next_page_token. Omit to\n request the first page." } }, "title": "ListStorageConnectionsRequest", "additionalProperties": false, "description": "Request to list storage connections." }, "elembio.cloud.v1.ListStorageConnectionsResponse": { "type": "object", "properties": { "storageConnections": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.StorageConnection" }, "title": "storage_connections", "description": "The storage connections on this page." }, "nextPageToken": { "type": "string", "title": "next_page_token", "description": "Token for the next page, or empty when there are no more results." } }, "title": "ListStorageConnectionsResponse", "additionalProperties": false, "description": "Response containing a page of storage connections." }, "elembio.cloud.v1.MultiomicsMetrics": { "type": "object", "properties": { "totalCellCount": { "type": [ "integer", "null" ], "title": "total_cell_count", "format": "int32" }, "totalCellConfluency": { "type": [ "number", "null" ], "title": "total_cell_confluency", "format": "float" }, "totalPercentAssigned": { "type": [ "number", "null" ], "title": "total_percent_assigned", "format": "float" } }, "title": "MultiomicsMetrics", "additionalProperties": false, "description": "Multiomics run metrics" }, "elembio.cloud.v1.MultiomicsSetup": { "type": "object", "properties": { "panel": { "title": "panel", "$ref": "#/components/schemas/elembio.cloud.v1.Panel" }, "kitType": { "type": "string", "title": "kit_type", "description": "The multiomics kit used for the run. Possible values: `cytoprofiling`,\n `direct_in_sample_sequencing`, `antibody_screening`, `tissue`,\n `protein_screening`." }, "kitId": { "type": "string", "title": "kit_id" }, "cartridge": { "title": "cartridge", "$ref": "#/components/schemas/elembio.cloud.v1.Cartridge" }, "wellLayout": { "type": "string", "title": "well_layout", "description": "The well plate layout used for the run. Possible values:\n `twelve_well_circle`, `twelve_well_square`, `two_well`, `one_well`,\n `twelve_well_standard`, `forty_eight_well`." }, "wells": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.Well" }, "title": "wells" }, "batches": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.Batch" }, "title": "batches" }, "smallCell": { "type": "boolean", "title": "small_cell" }, "tallCell": { "type": "boolean", "title": "tall_cell" }, "flowcell": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.Consumable" }, { "type": "null" } ], "title": "flowcell", "description": "Multiomics consumable details from run setup" }, "buffer": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.Consumable" }, { "type": "null" } ], "title": "buffer" }, "panelCartridge": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.Consumable" }, { "type": "null" } ], "title": "panel_cartridge" } }, "title": "MultiomicsSetup", "additionalProperties": false, "description": "Multiomics run setup/configuration fields" }, "elembio.cloud.v1.Output": { "type": "object", "properties": { "storageConnectionId": { "type": "string", "title": "storage_connection_id", "description": "Storage connection ID" }, "uri": { "type": "string", "title": "uri", "description": "Absolute URI of the output directory. May be empty if the\n upstream resource has not yet determined its output location.\n When non-empty, normalized to end in exactly one trailing slash.\n Example: s3://bucket/path/to/dir/" }, "kinds": { "type": "array", "items": { "type": "string" }, "title": "kinds", "description": "Content kinds present under uri. Possible values:\n \"fastq\", \"bam\", \"vcf\", \"cram\", \"parquet\",\n \"sequencing_run\", \"multiomics_run\".\n May be empty for in-flight executions: WorkflowRunSummary\n populates output kinds late in the lifecycle, so a running\n execution can briefly surface an Output with empty kinds even\n when the workflow definition declares them." } }, "title": "Output", "additionalProperties": false, "description": "Output describes where a resource's output files live and what\n kinds of content are produced. Used by both Run and Execution." }, "elembio.cloud.v1.Panel": { "type": "object", "properties": { "id": { "type": "string", "title": "id" }, "name": { "type": "string", "title": "name" }, "version": { "type": "string", "title": "version" } }, "title": "Panel", "additionalProperties": false, "description": "Panel information for multiomics runs" }, "elembio.cloud.v1.ReadConfig": { "type": "object", "properties": { "name": { "type": "string", "title": "name", "description": "R1, R2, I1, I2" }, "cycles": { "type": "integer", "title": "cycles", "format": "int32" }, "order": { "type": "integer", "title": "order", "format": "int32" } }, "title": "ReadConfig", "additionalProperties": false, "description": "Read configuration for sequencing" }, "elembio.cloud.v1.Run": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "Unique identifier for the run" }, "name": { "type": "string", "title": "name", "description": "Human-readable name of the run" }, "description": { "type": "string", "title": "description", "description": "Optional description" }, "type": { "type": "string", "title": "type", "description": "Type of run. Possible values: \"sequencing\", \"multiomics\"." }, "status": { "title": "status", "description": "Current status of the run", "$ref": "#/components/schemas/elembio.cloud.v1.RunStatus" }, "instrument": { "title": "instrument", "description": "Instrument that performed the run", "$ref": "#/components/schemas/elembio.cloud.v1.RunInstrument" }, "output": { "title": "output", "description": "Output location and content kinds for run data", "$ref": "#/components/schemas/elembio.cloud.v1.Output" }, "timeCreated": { "title": "time_created", "description": "Timestamps", "$ref": "#/components/schemas/google.protobuf.Timestamp" }, "timeStarted": { "oneOf": [ { "$ref": "#/components/schemas/google.protobuf.Timestamp" }, { "type": "null" } ], "title": "time_started" }, "timeCompleted": { "oneOf": [ { "$ref": "#/components/schemas/google.protobuf.Timestamp" }, { "type": "null" } ], "title": "time_completed" }, "timeUpdated": { "oneOf": [ { "$ref": "#/components/schemas/google.protobuf.Timestamp" }, { "type": "null" } ], "title": "time_updated" }, "tags": { "type": "array", "items": { "type": "string" }, "title": "tags", "description": "User-defined tags" }, "recipe": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.RunRecipe" }, { "type": "null" } ], "title": "recipe", "description": "Recipe used for the run (if an Element recipe was selected)" }, "manifest": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.RunManifest" }, { "type": "null" } ], "title": "manifest", "description": "Run manifest metadata.\n On ListRuns only filename is populated; on GetRun the full object\n (including download_url) is populated." }, "design": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.RunDesign" }, { "type": "null" } ], "title": "design", "description": "Design associated with the run (sequencing or multiomics)" }, "operator": { "type": "string", "title": "operator", "description": "User who operated (initiated) the run on the instrument" }, "setup": { "title": "setup", "description": "Run setup configuration, grouped by run type", "$ref": "#/components/schemas/elembio.cloud.v1.RunSetup" }, "metrics": { "title": "metrics", "description": "Run metrics/results, grouped by run type", "$ref": "#/components/schemas/elembio.cloud.v1.RunMetrics" } }, "title": "Run", "additionalProperties": false, "description": "A Run represents an instrument run (either sequencing or multiomics)" }, "elembio.cloud.v1.RunDesign": { "type": "object", "properties": { "id": { "type": "string", "title": "id" }, "name": { "type": "string", "title": "name" }, "kind": { "type": "string", "title": "kind", "description": "e.g., \"spike_in_panel\", \"diss_panel\", \"focus_spike_in_panel\"" } }, "title": "RunDesign", "additionalProperties": false, "description": "Design associated with a run" }, "elembio.cloud.v1.RunInstrument": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "Instrument identifier." }, "name": { "type": "string", "title": "name", "description": "Human-readable instrument name. Example: \"AV223501\"." }, "serialNumber": { "type": "string", "title": "serial_number", "description": "Instrument serial number. Example: \"AV223501\"." }, "model": { "type": "string", "title": "model", "description": "Instrument model as recorded for the run. Free-form text passed through\n from the run record; example: \"AVITI\"." }, "softwareVersion": { "type": "string", "title": "software_version", "description": "AOS (instrument operating system) software version at run time.\n Example: \"2.6.1\"." } }, "title": "RunInstrument", "additionalProperties": false, "description": "Instrument that performed a run. These fields are a snapshot captured at\n run time and may differ from the instrument's current state as returned by\n InstrumentService." }, "elembio.cloud.v1.RunManifest": { "type": "object", "properties": { "filename": { "type": "string", "title": "filename", "description": "Manifest filename" }, "description": { "type": "string", "title": "description", "description": "Description of the manifest" }, "timeUploaded": { "title": "time_uploaded", "description": "When the manifest was uploaded", "$ref": "#/components/schemas/google.protobuf.Timestamp" }, "downloadUrl": { "type": "string", "title": "download_url", "description": "Pre-signed URL for downloading the manifest CSV over HTTP GET.\n A short-lived credential; fetch promptly and do not persist it.\n Populated only on GetRun." } }, "title": "RunManifest", "additionalProperties": false, "description": "Manifest metadata for a run (only fully populated on GetRun)" }, "elembio.cloud.v1.RunMetrics": { "type": "object", "properties": { "sequencing": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.SequencingMetrics" }, { "type": "null" } ], "title": "sequencing" }, "multiomics": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.MultiomicsMetrics" }, { "type": "null" } ], "title": "multiomics" } }, "title": "RunMetrics", "additionalProperties": false, "description": "Run metrics/results, grouped by run type.\n Only one of the type-specific sub-messages will be populated per run." }, "elembio.cloud.v1.RunRecipe": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "Recipe identifier." }, "name": { "type": "string", "title": "name", "description": "Recipe name." } }, "title": "RunRecipe", "additionalProperties": false, "description": "Element recipe selected for a run." }, "elembio.cloud.v1.RunReference": { "type": "object", "properties": { "id": { "type": "string", "title": "id" }, "name": { "type": "string", "title": "name" }, "instrumentName": { "type": "string", "title": "instrument_name" }, "kitType": { "type": "string", "title": "kit_type", "description": "The run's kit. For multiomics runs, one of the multiomics kit values\n (`cytoprofiling`, `direct_in_sample_sequencing`, `antibody_screening`,\n `tissue`, `protein_screening`); for sequencing runs, the sequencing kit." }, "runType": { "type": "string", "title": "run_type", "description": "\"sequencing\" or \"multiomics\"" } }, "title": "RunReference", "additionalProperties": false, "description": "Reference to an instrument run" }, "elembio.cloud.v1.RunSetup": { "type": "object", "properties": { "sequencing": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.SequencingSetup" }, { "type": "null" } ], "title": "sequencing" }, "multiomics": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.MultiomicsSetup" }, { "type": "null" } ], "title": "multiomics" } }, "title": "RunSetup", "additionalProperties": false, "description": "Run setup configuration, grouped by run type.\n Only one of the type-specific sub-messages will be populated per run." }, "elembio.cloud.v1.RunStatus": { "type": "string", "title": "RunStatus", "enum": [ "RUN_STATUS_UNSPECIFIED", "RUN_STATUS_CREATED", "RUN_STATUS_PRIMING", "RUN_STATUS_PRIMED", "RUN_STATUS_SEQUENCING", "RUN_STATUS_RUNNING", "RUN_STATUS_PAUSING", "RUN_STATUS_PAUSED", "RUN_STATUS_STOPPING", "RUN_STATUS_SEQUENCED", "RUN_STATUS_COMPLETED", "RUN_STATUS_FAILED", "RUN_STATUS_STOPPED", "RUN_STATUS_DISCARDED" ], "description": "Status of a run, matching the status shown in the EBC UI." }, "elembio.cloud.v1.S3Credentials": { "type": "object", "properties": { "region": { "type": "string", "title": "region", "description": "AWS region. Example: \"us-west-2\"." }, "bucket": { "type": "string", "title": "bucket", "description": "S3 bucket name." }, "prefix": { "type": [ "string", "null" ], "title": "prefix", "description": "Key prefix the credentials are scoped to — bucket-absolute, since\n this value is consumed directly by the AWS CLI / SDK. Distinct from\n the request-side `prefix`, which is connection-relative." }, "accessKeyId": { "type": "string", "title": "access_key_id", "description": "Temporary AWS access key ID" }, "secretAccessKey": { "type": "string", "title": "secret_access_key", "description": "Temporary AWS secret access key" }, "sessionToken": { "type": "string", "title": "session_token", "description": "STS session token" }, "expiration": { "title": "expiration", "description": "When the credentials expire", "$ref": "#/components/schemas/google.protobuf.Timestamp" } }, "title": "S3Credentials", "additionalProperties": false, "description": "Temporary read-only AWS S3 credentials scoped to a bucket and prefix.\n Use with the AWS CLI, AWS SDK, or any S3-compatible tool. The credentials\n expire at the time given by expiration; request new credentials when they\n near expiry." }, "elembio.cloud.v1.SequencingMetrics": { "type": "object", "properties": { "phixAlignmentRate": { "type": [ "number", "null" ], "title": "phix_alignment_rate", "format": "float" }, "totalYield": { "type": [ "integer", "string", "null" ], "title": "total_yield", "format": "int64" }, "totalReads": { "type": [ "integer", "string", "null" ], "title": "total_reads", "format": "int64" }, "estimatedReads": { "type": [ "integer", "string", "null" ], "title": "estimated_reads", "format": "int64" }, "q30": { "type": [ "number", "null" ], "title": "q30", "format": "float" }, "q40": { "type": [ "number", "null" ], "title": "q40", "format": "float" }, "avgQ": { "type": [ "number", "null" ], "title": "avg_q", "format": "float" }, "errorRate": { "type": [ "number", "null" ], "title": "error_rate", "format": "float" }, "q50": { "type": [ "number", "null" ], "title": "q50", "format": "float" } }, "title": "SequencingMetrics", "additionalProperties": false, "description": "Sequencing run metrics" }, "elembio.cloud.v1.SequencingSetup": { "type": "object", "properties": { "kitName": { "type": "string", "title": "kit_name" }, "kitPartNumber": { "type": "string", "title": "kit_part_number" }, "libraryStructure": { "type": "string", "title": "library_structure", "description": "\"circular\" or \"linear\"" }, "prepType": { "type": "string", "title": "prep_type", "description": "e.g., \"adept\", \"elevate\"" }, "dualLibrary": { "type": "boolean", "title": "dual_library" }, "reads": { "type": "array", "items": { "$ref": "#/components/schemas/elembio.cloud.v1.ReadConfig" }, "title": "reads" }, "chemistryVersion": { "type": "string", "title": "chemistry_version" }, "pmgShift": { "type": [ "integer", "null" ], "title": "pmg_shift", "format": "int32", "description": "Advanced settings (AOS 2.6.0+)" }, "filterMask": { "type": [ "string", "null" ], "title": "filter_mask" }, "polonyDensity": { "type": [ "string", "null" ], "title": "polony_density", "description": "\"standard\" or \"high\"" }, "lowDiversity": { "type": "boolean", "title": "low_diversity", "description": "Low Diversity High Multiplex" }, "panel": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.Panel" }, { "type": "null" } ], "title": "panel", "description": "Panel information (AOS 2.7.0+; run-level pre-3.5, per-lane 3.5+)" }, "flowcell": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.Consumable" }, { "type": "null" } ], "title": "flowcell", "description": "Sequencing consumable details from run setup" }, "buffer": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.Consumable" }, { "type": "null" } ], "title": "buffer" }, "sequencingCartridge": { "oneOf": [ { "$ref": "#/components/schemas/elembio.cloud.v1.Consumable" }, { "type": "null" } ], "title": "sequencing_cartridge" } }, "title": "SequencingSetup", "additionalProperties": false, "description": "Sequencing run setup/configuration fields" }, "elembio.cloud.v1.StorageConnection": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "Unique identifier for the connection." }, "name": { "type": "string", "title": "name", "description": "Human-readable connection name." }, "type": { "type": "string", "title": "type", "description": "Storage backend type. Possible values: \"s3\", \"gcs\", \"dnanexus\"." }, "status": { "title": "status", "description": "Current health status of the connection.", "$ref": "#/components/schemas/elembio.cloud.v1.StorageConnectionStatus" }, "uri": { "type": "string", "title": "uri", "description": "Storage URI rooted at the connection. Examples: \"s3://bucket/prefix\",\n \"gcs://bucket/prefix\"." }, "timeCreated": { "title": "time_created", "description": "When the connection was created.", "$ref": "#/components/schemas/google.protobuf.Timestamp" }, "timeUpdated": { "title": "time_updated", "description": "When the connection was last updated.", "$ref": "#/components/schemas/google.protobuf.Timestamp" } }, "title": "StorageConnection", "additionalProperties": false, "description": "A StorageConnection represents a configured cloud storage location." }, "elembio.cloud.v1.StorageConnectionStatus": { "type": "string", "title": "StorageConnectionStatus", "enum": [ "STORAGE_CONNECTION_STATUS_UNSPECIFIED", "STORAGE_CONNECTION_STATUS_CONNECTED", "STORAGE_CONNECTION_STATUS_WARNING", "STORAGE_CONNECTION_STATUS_FAILED" ], "description": "Health status of a storage connection." }, "elembio.cloud.v1.UserSummary": { "type": "object", "properties": { "id": { "type": "string", "title": "id", "description": "User identifier." }, "email": { "type": "string", "title": "email", "description": "User's email address." }, "name": { "type": "string", "title": "name", "description": "User's display name." } }, "title": "UserSummary", "additionalProperties": false, "description": "UserSummary identifies a user for attribution on a resource." }, "elembio.cloud.v1.Well": { "type": "object", "properties": { "location": { "type": "string", "title": "location", "description": "e.g., \"A1\", \"B2\"" }, "label": { "type": "string", "title": "label" } }, "title": "Well", "additionalProperties": false, "description": "Well information for multiomics runs" }, "elembio.cloud.v1.Workflow": { "type": "object", "properties": { "name": { "type": "string", "title": "name" }, "version": { "type": "string", "title": "version" } }, "title": "Workflow", "additionalProperties": false, "description": "Workflow information" }, "google.protobuf.Timestamp": { "type": "string", "examples": [ "2023-01-15T01:30:15.01Z", "2024-12-25T12:00:00Z" ], "format": "date-time", "description": "A Timestamp represents a point in time independent of any time zone or local\n calendar, encoded as a count of seconds and fractions of seconds at\n nanosecond resolution. The count is relative to an epoch at UTC midnight on\n January 1, 1970, in the proleptic Gregorian calendar which extends the\n Gregorian calendar backwards to year one.\n\n All minutes are 60 seconds long. Leap seconds are \"smeared\" so that no leap\n second table is needed for interpretation, using a [24-hour linear\n smear](https://developers.google.com/time/smear).\n\n The range is from 0001-01-01T00:00:00Z to 9999-12-31T23:59:59.999999999Z. By\n restricting to that range, we ensure that we can convert to and from [RFC\n 3339](https://www.ietf.org/rfc/rfc3339.txt) date strings.\n\n # Examples\n\n Example 1: Compute Timestamp from POSIX `time()`.\n\n Timestamp timestamp;\n timestamp.set_seconds(time(NULL));\n timestamp.set_nanos(0);\n\n Example 2: Compute Timestamp from POSIX `gettimeofday()`.\n\n struct timeval tv;\n gettimeofday(&tv, NULL);\n\n Timestamp timestamp;\n timestamp.set_seconds(tv.tv_sec);\n timestamp.set_nanos(tv.tv_usec * 1000);\n\n Example 3: Compute Timestamp from Win32 `GetSystemTimeAsFileTime()`.\n\n FILETIME ft;\n GetSystemTimeAsFileTime(&ft);\n UINT64 ticks = (((UINT64)ft.dwHighDateTime) << 32) | ft.dwLowDateTime;\n\n // A Windows tick is 100 nanoseconds. Windows epoch 1601-01-01T00:00:00Z\n // is 11644473600 seconds before Unix epoch 1970-01-01T00:00:00Z.\n Timestamp timestamp;\n timestamp.set_seconds((INT64) ((ticks / 10000000) - 11644473600LL));\n timestamp.set_nanos((INT32) ((ticks % 10000000) * 100));\n\n Example 4: Compute Timestamp from Java `System.currentTimeMillis()`.\n\n long millis = System.currentTimeMillis();\n\n Timestamp timestamp = Timestamp.newBuilder().setSeconds(millis / 1000)\n .setNanos((int) ((millis % 1000) * 1000000)).build();\n\n Example 5: Compute Timestamp from Java `Instant.now()`.\n\n Instant now = Instant.now();\n\n Timestamp timestamp =\n Timestamp.newBuilder().setSeconds(now.getEpochSecond())\n .setNanos(now.getNano()).build();\n\n Example 6: Compute Timestamp from current time in Python.\n\n timestamp = Timestamp()\n timestamp.GetCurrentTime()\n\n # JSON Mapping\n\n In JSON format, the Timestamp type is encoded as a string in the\n [RFC 3339](https://www.ietf.org/rfc/rfc3339.txt) format. That is, the\n format is \"{year}-{month}-{day}T{hour}:{min}:{sec}[.{frac_sec}]Z\"\n where {year} is always expressed using four digits while {month}, {day},\n {hour}, {min}, and {sec} are zero-padded to two digits each. The fractional\n seconds, which can go up to 9 digits (i.e. up to 1 nanosecond resolution),\n are optional. The \"Z\" suffix indicates the timezone (\"UTC\"); the timezone\n is required. A ProtoJSON serializer should always use UTC (as indicated by\n \"Z\") when printing the Timestamp type and a ProtoJSON parser should be\n able to accept both UTC and other timezones (as indicated by an offset).\n\n For example, \"2017-01-15T01:30:15.01Z\" encodes 15.01 seconds past\n 01:30 UTC on January 15, 2017.\n\n In JavaScript, one can convert a Date object to this format using the\n standard\n [toISOString()](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Date/toISOString)\n method. In Python, a standard `datetime.datetime` object can be converted\n to this format using\n [`strftime`](https://docs.python.org/2/library/time.html#time.strftime) with\n the time format spec '%Y-%m-%dT%H:%M:%S.%fZ'. Likewise, in Java, one can use\n the Joda Time's [`ISODateTimeFormat.dateTime()`](\n http://joda-time.sourceforge.net/apidocs/org/joda/time/format/ISODateTimeFormat.html#dateTime()\n ) to obtain a formatter capable of generating timestamps in this format." } } }, "paths": { "/v1/auth": { "get": { "tags": [ "AuthService" ], "summary": "GetAuth", "description": "Return the tenant the current API key belongs to. This endpoint requires a\n valid API key but no additional scope, so it is a convenient way to verify\n that a key is working.", "operationId": "AuthService_GetAuth", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetAuthResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/executions": { "get": { "tags": [ "ExecutionService" ], "summary": "ListExecutions", "description": "List executions accessible to the authenticated tenant, optionally\n filtered.", "operationId": "ExecutionService_ListExecutions", "parameters": [ { "name": "filter", "in": "query", "description": "Search and filter expression. Space-separated `keyword:value` terms are\n ANDed together; bare text with no keyword searches all string fields. For\n date fields, replace the colon with a comparison operator (`>=`, `<=`,\n `>`, `<`, `!=`). List alternatives for one keyword with commas, e.g.\n `status:running,pending`. Dates accept ISO-8601 or relative offsets such\n as `24h`, `7d`, or `1mo`.\n\n Filterable keywords:\n\n - **String:** `name`, `input.run.id`, `input.run.name`, `input.run.instrument_name`, `input.execution.id`, `input.execution.name`, `flow.name`, `workflow.name`, `started_by`\n - **Enum:** `status`, `platform` (`aws_omics`, `seqera`, `dnanexus`, `catalyst`), `output.kind` (`fastq`, `bam`, `vcf`, `cram`, `parquet`)\n - **Date:** `time_created`, `time_started`, `time_completed`, `time_updated`\n\n Examples:\n\n - `workflow.name:bases2fastq status:running`\n - `platform:seqera output.kind:fastq time_completed>=24h`", "schema": { "type": "string", "title": "filter", "description": "Search and filter expression. Space-separated `keyword:value` terms are\n ANDed together; bare text with no keyword searches all string fields. For\n date fields, replace the colon with a comparison operator (`>=`, `<=`,\n `>`, `<`, `!=`). List alternatives for one keyword with commas, e.g.\n `status:running,pending`. Dates accept ISO-8601 or relative offsets such\n as `24h`, `7d`, or `1mo`.\n\n Filterable keywords:\n\n - **String:** `name`, `input.run.id`, `input.run.name`, `input.run.instrument_name`, `input.execution.id`, `input.execution.name`, `flow.name`, `workflow.name`, `started_by`\n - **Enum:** `status`, `platform` (`aws_omics`, `seqera`, `dnanexus`, `catalyst`), `output.kind` (`fastq`, `bam`, `vcf`, `cram`, `parquet`)\n - **Date:** `time_created`, `time_started`, `time_completed`, `time_updated`\n\n Examples:\n\n - `workflow.name:bases2fastq status:running`\n - `platform:seqera output.kind:fastq time_completed>=24h`" } }, { "name": "pageSize", "in": "query", "description": "Maximum number of executions to return (default: 100, max: 1000)", "schema": { "type": "integer", "title": "page_size", "format": "int32", "description": "Maximum number of executions to return (default: 100, max: 1000)" } }, { "name": "pageToken", "in": "query", "description": "Token for pagination", "schema": { "type": "string", "title": "page_token", "description": "Token for pagination" } }, { "name": "includeTotalCount", "in": "query", "description": "If true, include total_count in the response (adds a count query)", "schema": { "type": "boolean", "title": "include_total_count", "description": "If true, include total_count in the response (adds a count query)" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.ListExecutionsResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/executions/{execution_id}/credentials": { "get": { "tags": [ "ExecutionService" ], "summary": "GetExecutionDownloadCredentials", "description": "Get temporary, read-only S3 credentials scoped to an execution's storage\n location. Use these for bulk or repeated downloads via the AWS CLI or SDK\n instead of per-object presigned URLs.", "operationId": "ExecutionService_GetExecutionDownloadCredentials", "parameters": [ { "name": "execution_id", "in": "path", "description": "The execution ID", "required": true, "schema": { "type": "string", "title": "execution_id", "description": "The execution ID" } }, { "name": "prefix", "in": "query", "description": "Optional path prefix within the execution to scope credentials to.\n Execution-relative, identical semantics to\n ListExecutionFilesRequest.prefix. \"..\" segments are rejected.\n When omitted, credentials are scoped to the whole execution (the\n execution root).", "schema": { "type": "string", "title": "prefix", "description": "Optional path prefix within the execution to scope credentials to.\n Execution-relative, identical semantics to\n ListExecutionFilesRequest.prefix. \"..\" segments are rejected.\n When omitted, credentials are scoped to the whole execution (the\n execution root)." } }, { "name": "expirationSeconds", "in": "query", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected.", "schema": { "type": "integer", "title": "expiration_seconds", "format": "int32", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetExecutionDownloadCredentialsResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/executions/{execution_id}/files": { "get": { "tags": [ "ExecutionService" ], "summary": "ListExecutionFiles", "description": "List the files produced by an execution, drawn from the execution's\n storage location.", "operationId": "ExecutionService_ListExecutionFiles", "parameters": [ { "name": "execution_id", "in": "path", "description": "The execution ID", "required": true, "schema": { "type": "string", "title": "execution_id", "description": "The execution ID" } }, { "name": "prefix", "in": "query", "description": "Path prefix within the execution, e.g. \"visualization/\" or \"Stats/foo\".\n The execution is a self-contained namespace: paths do not include any\n bucket-level or workflow-level layout. Round-trips with File.path\n returned by this RPC. \"..\" segments are rejected.\n Optional: when omitted, lists the whole execution (the execution root).", "schema": { "type": "string", "title": "prefix", "description": "Path prefix within the execution, e.g. \"visualization/\" or \"Stats/foo\".\n The execution is a self-contained namespace: paths do not include any\n bucket-level or workflow-level layout. Round-trips with File.path\n returned by this RPC. \"..\" segments are rejected.\n Optional: when omitted, lists the whole execution (the execution root)." } }, { "name": "recursive", "in": "query", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level", "schema": { "type": "boolean", "title": "recursive", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level" } }, { "name": "pageSize", "in": "query", "description": "Maximum number of files to return per page (default: 1000, max: 1000)", "schema": { "type": "integer", "title": "page_size", "format": "int32", "description": "Maximum number of files to return per page (default: 1000, max: 1000)" } }, { "name": "pageToken", "in": "query", "description": "Continuation token from previous response (passthrough from storage)", "schema": { "type": "string", "title": "page_token", "description": "Continuation token from previous response (passthrough from storage)" } }, { "name": "includeDownloadUrl", "in": "query", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetExecutionDownloadCredentials when\n long-lived bulk access is required.", "schema": { "type": "boolean", "title": "include_download_url", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetExecutionDownloadCredentials when\n long-lived bulk access is required." } }, { "name": "downloadUrlExpirationSeconds", "in": "query", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days.", "schema": { "type": "integer", "title": "download_url_expiration_seconds", "format": "int32", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days." } }, { "name": "includeDownloadChecksum", "in": "query", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field.", "schema": { "type": "boolean", "title": "include_download_checksum", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.ListExecutionFilesResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/executions/{execution_id}/logs": { "get": { "tags": [ "ExecutionService" ], "summary": "GetExecutionLogs", "description": "Get the log and error output from the compute platform for an execution.\n Requires the \"executions:logs\" scope.", "operationId": "ExecutionService_GetExecutionLogs", "parameters": [ { "name": "execution_id", "in": "path", "description": "The execution ID", "required": true, "schema": { "type": "string", "title": "execution_id", "description": "The execution ID" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetExecutionLogsResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/executions/{id}": { "get": { "tags": [ "ExecutionService" ], "summary": "GetExecution", "description": "Get a single execution by its ID.", "operationId": "ExecutionService_GetExecution", "parameters": [ { "name": "id", "in": "path", "description": "The unique identifier of the execution", "required": true, "schema": { "type": "string", "title": "id", "description": "The unique identifier of the execution" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetExecutionResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/instruments": { "get": { "tags": [ "InstrumentService" ], "summary": "ListInstruments", "description": "List instruments registered to the authenticated tenant.", "operationId": "InstrumentService_ListInstruments", "parameters": [ { "name": "pageSize", "in": "query", "description": "Maximum number of instruments to return. Defaults to 100; values above\n 1000 are capped at 1000.", "schema": { "type": "integer", "title": "page_size", "format": "int32", "description": "Maximum number of instruments to return. Defaults to 100; values above\n 1000 are capped at 1000." } }, { "name": "pageToken", "in": "query", "description": "Pagination token from a previous response's next_page_token. Omit to\n request the first page.", "schema": { "type": "string", "title": "page_token", "description": "Pagination token from a previous response's next_page_token. Omit to\n request the first page." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.ListInstrumentsResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/instruments/{serial_number}": { "get": { "tags": [ "InstrumentService" ], "summary": "GetInstrument", "description": "Get a single instrument by its serial number.", "operationId": "InstrumentService_GetInstrument", "parameters": [ { "name": "serial_number", "in": "path", "description": "Serial number of the instrument to retrieve. Example: \"AV223501\".", "required": true, "schema": { "type": "string", "title": "serial_number", "description": "Serial number of the instrument to retrieve. Example: \"AV223501\"." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetInstrumentResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/runs": { "get": { "tags": [ "RunService" ], "summary": "ListRuns", "description": "List runs accessible to the authenticated tenant, optionally filtered.", "operationId": "RunService_ListRuns", "parameters": [ { "name": "filter", "in": "query", "description": "Search and filter expression. Space-separated `keyword:value` terms are\n ANDed together; bare text with no keyword searches all string fields. For\n numeric and date fields, replace the colon with a comparison operator\n (`>=`, `<=`, `>`, `<`, `!=`). List alternatives for one keyword with\n commas, e.g. `status:completed,failed`. Dates accept ISO-8601 or relative\n offsets such as `7d` or `1mo`.\n\n Filterable keywords:\n\n - **String:** `name`, `id`, `description`, `tags`, `instrument.name`, `instrument.serial_number`, `instrument.model`, `storage.connection_id`, `setup.sequencing.kit_name`, `setup.sequencing.library_structure`, `setup.sequencing.prep_type`, `setup.sequencing.polony_density`, `setup.sequencing.filter_mask`, `setup.sequencing.panel.name`, `setup.multiomics.panel.name`, `setup.multiomics.cartridge.name`\n - **Enum:** `type` (`sequencing`, `multiomics`), `status`, `output.kind` (`sequencing_run`, `multiomics_run`; an alias for `type`), `setup.multiomics.kit_type` (`cytoprofiling`, `direct_in_sample_sequencing`, `antibody_screening`, `tissue`, `protein_screening`), `setup.multiomics.well_layout` (`twelve_well_circle`, `twelve_well_square`, `two_well`, `one_well`, `twelve_well_standard`, `forty_eight_well`)\n - **Date:** `time_created`, `time_started`, `time_completed`, `time_updated`\n - **Numeric:** `metrics.sequencing.total_reads`, `metrics.sequencing.total_yield`, `metrics.sequencing.estimated_reads`, `metrics.sequencing.q30`, `metrics.sequencing.q40`, `metrics.sequencing.q50`, `metrics.sequencing.avg_q`, `metrics.sequencing.error_rate`, `metrics.sequencing.phix_alignment_rate`, `metrics.multiomics.total_cell_count`, `metrics.multiomics.total_cell_confluency`, `metrics.multiomics.total_percent_assigned`, `setup.sequencing.pmg_shift`\n - **Boolean:** `setup.sequencing.low_diversity`\n\n Examples:\n\n - `type:sequencing status:completed time_completed>=7d`\n - `instrument.serial_number:AV223501 metrics.sequencing.q30>=90`", "schema": { "type": "string", "title": "filter", "description": "Search and filter expression. Space-separated `keyword:value` terms are\n ANDed together; bare text with no keyword searches all string fields. For\n numeric and date fields, replace the colon with a comparison operator\n (`>=`, `<=`, `>`, `<`, `!=`). List alternatives for one keyword with\n commas, e.g. `status:completed,failed`. Dates accept ISO-8601 or relative\n offsets such as `7d` or `1mo`.\n\n Filterable keywords:\n\n - **String:** `name`, `id`, `description`, `tags`, `instrument.name`, `instrument.serial_number`, `instrument.model`, `storage.connection_id`, `setup.sequencing.kit_name`, `setup.sequencing.library_structure`, `setup.sequencing.prep_type`, `setup.sequencing.polony_density`, `setup.sequencing.filter_mask`, `setup.sequencing.panel.name`, `setup.multiomics.panel.name`, `setup.multiomics.cartridge.name`\n - **Enum:** `type` (`sequencing`, `multiomics`), `status`, `output.kind` (`sequencing_run`, `multiomics_run`; an alias for `type`), `setup.multiomics.kit_type` (`cytoprofiling`, `direct_in_sample_sequencing`, `antibody_screening`, `tissue`, `protein_screening`), `setup.multiomics.well_layout` (`twelve_well_circle`, `twelve_well_square`, `two_well`, `one_well`, `twelve_well_standard`, `forty_eight_well`)\n - **Date:** `time_created`, `time_started`, `time_completed`, `time_updated`\n - **Numeric:** `metrics.sequencing.total_reads`, `metrics.sequencing.total_yield`, `metrics.sequencing.estimated_reads`, `metrics.sequencing.q30`, `metrics.sequencing.q40`, `metrics.sequencing.q50`, `metrics.sequencing.avg_q`, `metrics.sequencing.error_rate`, `metrics.sequencing.phix_alignment_rate`, `metrics.multiomics.total_cell_count`, `metrics.multiomics.total_cell_confluency`, `metrics.multiomics.total_percent_assigned`, `setup.sequencing.pmg_shift`\n - **Boolean:** `setup.sequencing.low_diversity`\n\n Examples:\n\n - `type:sequencing status:completed time_completed>=7d`\n - `instrument.serial_number:AV223501 metrics.sequencing.q30>=90`" } }, { "name": "pageSize", "in": "query", "description": "Maximum number of runs to return (default: 100, max: 1000)", "schema": { "type": "integer", "title": "page_size", "format": "int32", "description": "Maximum number of runs to return (default: 100, max: 1000)" } }, { "name": "pageToken", "in": "query", "description": "Token for pagination", "schema": { "type": "string", "title": "page_token", "description": "Token for pagination" } }, { "name": "includeTotalCount", "in": "query", "description": "If true, include total_count in the response (adds a count query)", "schema": { "type": "boolean", "title": "include_total_count", "description": "If true, include total_count in the response (adds a count query)" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.ListRunsResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/runs/{id}": { "get": { "tags": [ "RunService" ], "summary": "GetRun", "description": "Get a single run by its ID.", "operationId": "RunService_GetRun", "parameters": [ { "name": "id", "in": "path", "description": "The unique identifier of the run", "required": true, "schema": { "type": "string", "title": "id", "description": "The unique identifier of the run" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetRunResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/runs/{run_id}/credentials": { "get": { "tags": [ "RunService" ], "summary": "GetRunDownloadCredentials", "description": "Get temporary, read-only S3 credentials scoped to a run's storage\n location. Use these for bulk or repeated downloads via the AWS CLI or\n SDK instead of per-object presigned URLs.", "operationId": "RunService_GetRunDownloadCredentials", "parameters": [ { "name": "run_id", "in": "path", "description": "The run ID", "required": true, "schema": { "type": "string", "title": "run_id", "description": "The run ID" } }, { "name": "prefix", "in": "query", "description": "Optional path prefix within the run to scope credentials to.\n Run-relative, identical semantics to ListRunFilesRequest.prefix.\n \"..\" segments are rejected. When omitted, credentials are scoped to\n the whole run (the run root).", "schema": { "type": "string", "title": "prefix", "description": "Optional path prefix within the run to scope credentials to.\n Run-relative, identical semantics to ListRunFilesRequest.prefix.\n \"..\" segments are rejected. When omitted, credentials are scoped to\n the whole run (the run root)." } }, { "name": "expirationSeconds", "in": "query", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected.", "schema": { "type": "integer", "title": "expiration_seconds", "format": "int32", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetRunDownloadCredentialsResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/runs/{run_id}/files": { "get": { "tags": [ "RunService" ], "summary": "ListRunFiles", "description": "List the files produced by a run, drawn from the run's storage location.", "operationId": "RunService_ListRunFiles", "parameters": [ { "name": "run_id", "in": "path", "description": "The run ID", "required": true, "schema": { "type": "string", "title": "run_id", "description": "The run ID" } }, { "name": "prefix", "in": "query", "description": "Path prefix within the run, e.g. \"visualization/\" or \"Stats/foo\".\n The run is a self-contained namespace: paths do not include any\n bucket-level or workflow-level layout. Round-trips with File.path\n returned by this RPC. \"..\" segments are rejected.\n Optional: when omitted, lists the whole run (the run root).", "schema": { "type": "string", "title": "prefix", "description": "Path prefix within the run, e.g. \"visualization/\" or \"Stats/foo\".\n The run is a self-contained namespace: paths do not include any\n bucket-level or workflow-level layout. Round-trips with File.path\n returned by this RPC. \"..\" segments are rejected.\n Optional: when omitted, lists the whole run (the run root)." } }, { "name": "recursive", "in": "query", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level", "schema": { "type": "boolean", "title": "recursive", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level" } }, { "name": "pageSize", "in": "query", "description": "Maximum number of files to return per page (default: 1000, max: 1000)", "schema": { "type": "integer", "title": "page_size", "format": "int32", "description": "Maximum number of files to return per page (default: 1000, max: 1000)" } }, { "name": "pageToken", "in": "query", "description": "Continuation token from previous response (passthrough from storage)", "schema": { "type": "string", "title": "page_token", "description": "Continuation token from previous response (passthrough from storage)" } }, { "name": "includeDownloadUrl", "in": "query", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetRunDownloadCredentials when long-lived\n bulk access is required.", "schema": { "type": "boolean", "title": "include_download_url", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetRunDownloadCredentials when long-lived\n bulk access is required." } }, { "name": "downloadUrlExpirationSeconds", "in": "query", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days.", "schema": { "type": "integer", "title": "download_url_expiration_seconds", "format": "int32", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days." } }, { "name": "includeDownloadChecksum", "in": "query", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field.", "schema": { "type": "boolean", "title": "include_download_checksum", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.ListRunFilesResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/storage-connections": { "get": { "tags": [ "StorageConnectionService" ], "summary": "ListStorageConnections", "description": "List storage connections accessible to the authenticated tenant.", "operationId": "StorageConnectionService_ListStorageConnections", "parameters": [ { "name": "pageSize", "in": "query", "description": "Maximum number of connections to return. Defaults to 100; values above\n 1000 are capped at 1000.", "schema": { "type": "integer", "title": "page_size", "format": "int32", "description": "Maximum number of connections to return. Defaults to 100; values above\n 1000 are capped at 1000." } }, { "name": "pageToken", "in": "query", "description": "Pagination token from a previous response's next_page_token. Omit to\n request the first page.", "schema": { "type": "string", "title": "page_token", "description": "Pagination token from a previous response's next_page_token. Omit to\n request the first page." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.ListStorageConnectionsResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/storage-connections/{id}": { "get": { "tags": [ "StorageConnectionService" ], "summary": "GetStorageConnection", "description": "Get a single storage connection by its ID.", "operationId": "StorageConnectionService_GetStorageConnection", "parameters": [ { "name": "id", "in": "path", "description": "ID of the storage connection to retrieve.", "required": true, "schema": { "type": "string", "title": "id", "description": "ID of the storage connection to retrieve." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetStorageConnectionResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/storage-connections/{storage_connection_id}/credentials": { "get": { "tags": [ "StorageConnectionService" ], "summary": "GetDownloadCredentials", "description": "Get temporary, read-only S3 credentials scoped to a storage connection.\n Use these for bulk or repeated downloads via the AWS CLI or SDK instead\n of per-object presigned URLs.", "operationId": "StorageConnectionService_GetDownloadCredentials", "parameters": [ { "name": "storage_connection_id", "in": "path", "required": true, "schema": { "type": "string", "title": "storage_connection_id", "description": "The storage connection ID" } }, { "name": "prefix", "in": "query", "description": "Prefix to scope credentials to a subdirectory, relative to the storage\n connection's configured root. Matches the --prefix semantics of ListFiles:\n optional for an unrestricted key (omitted ⇒ connection root), but required\n and bounded to scope for a key scoped to a path prefix — omitting it or\n naming one outside the scope returns PermissionDenied with the allowed\n prefix(es) (`allowed_prefixes` metadata).", "schema": { "type": "string", "title": "prefix", "description": "Prefix to scope credentials to a subdirectory, relative to the storage\n connection's configured root. Matches the --prefix semantics of ListFiles:\n optional for an unrestricted key (omitted ⇒ connection root), but required\n and bounded to scope for a key scoped to a path prefix — omitting it or\n naming one outside the scope returns PermissionDenied with the allowed\n prefix(es) (`allowed_prefixes` metadata)." } }, { "name": "expirationSeconds", "in": "query", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected.", "schema": { "type": "integer", "title": "expiration_seconds", "format": "int32", "description": "Lifetime of the returned credentials, in seconds. Optional; defaults to\n 1 hour (when 0 or unset). Minimum 900s. Capped by AWS: up to 36h (129600s)\n for federation-token connections, or the role's MaxSessionDuration (12h\n typical) for role-backed connections. Values below the minimum or above the\n cap are rejected." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.GetDownloadCredentialsResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/v1/storage-connections/{storage_connection_id}/files": { "get": { "tags": [ "StorageConnectionService" ], "summary": "ListFiles", "description": "List files in a storage connection. Supports prefix filtering and, when\n recursive is false, delimiter-based hierarchical listing.", "operationId": "StorageConnectionService_ListFiles", "parameters": [ { "name": "storage_connection_id", "in": "path", "required": true, "schema": { "type": "string", "title": "storage_connection_id", "description": "The storage connection ID to browse" } }, { "name": "prefix", "in": "query", "description": "Path prefix relative to the storage connection's configured root,\n directory-shape with implicit trailing \"/\". The connection's saved\n sub-prefix (if any) is not part of this value — it's an\n implementation detail of the connection.\n Example: \"A24-S2/run-001/\". Round-trips with File.path.\n For an unrestricted key, optional: omitting it lists from the connection\n root. For a key scoped to a path prefix, a prefix WITHIN the scope is\n required: omitting it, or supplying one outside the scope, returns\n PermissionDenied with the allowed prefix(es) in the error\n (`allowed_prefixes` metadata).", "schema": { "type": "string", "title": "prefix", "description": "Path prefix relative to the storage connection's configured root,\n directory-shape with implicit trailing \"/\". The connection's saved\n sub-prefix (if any) is not part of this value — it's an\n implementation detail of the connection.\n Example: \"A24-S2/run-001/\". Round-trips with File.path.\n For an unrestricted key, optional: omitting it lists from the connection\n root. For a key scoped to a path prefix, a prefix WITHIN the scope is\n required: omitting it, or supplying one outside the scope, returns\n PermissionDenied with the allowed prefix(es) in the error\n (`allowed_prefixes` metadata)." } }, { "name": "recursive", "in": "query", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level", "schema": { "type": "boolean", "title": "recursive", "description": "If true, list all files recursively under the prefix (default: true)\n If false, list only files and subdirectories at the current level" } }, { "name": "pageSize", "in": "query", "description": "Maximum number of files to return per page (default: 1000, max: 1000)\n Note: This is passed through to the underlying storage system", "schema": { "type": "integer", "title": "page_size", "format": "int32", "description": "Maximum number of files to return per page (default: 1000, max: 1000)\n Note: This is passed through to the underlying storage system" } }, { "name": "pageToken", "in": "query", "description": "Continuation token from previous response\n This is an opaque token from the underlying storage system", "schema": { "type": "string", "title": "page_token", "description": "Continuation token from previous response\n This is an opaque token from the underlying storage system" } }, { "name": "includeDownloadUrl", "in": "query", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetDownloadCredentials when long-lived bulk\n access is required.", "schema": { "type": "boolean", "title": "include_download_url", "description": "If true, populate File.download_url (a presigned URL) on each returned\n file. Defaults to false. Set to true only when the caller intends to\n fetch file content from the response: generating presigned URLs has a\n per-object cost and the URLs themselves are credentials with a\n multi-hour lifetime. Use GetDownloadCredentials when long-lived bulk\n access is required." } }, { "name": "downloadUrlExpirationSeconds", "in": "query", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days.", "schema": { "type": "integer", "title": "download_url_expiration_seconds", "format": "int32", "description": "Lifetime of the presigned download_url, in seconds. Optional; defaults to\n 1 hour. Only applies when include_download_url = true. Max 7 days." } }, { "name": "includeDownloadChecksum", "in": "query", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field.", "schema": { "type": "boolean", "title": "include_download_checksum", "description": "If true, presign each download_url with S3 ChecksumMode=ENABLED so the\n object's stored checksum is returned on the GET (in the\n x-amz-checksum- response header) and a client can verify download\n integrity in a single streaming pass. Defaults false; has no effect unless\n include_download_url = true. When enabled the presigned URL signs the\n x-amz-checksum-mode request header, so the fetch MUST send\n x-amz-checksum-mode:ENABLED — a plain GET that omits it fails with HTTP\n 403. Best-effort: objects stored without a checksum return none.\n\n Applies only to AWS S3-backed storage connections; other storage backends\n do not presign S3 GETs and silently ignore this field." } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/elembio.cloud.v1.ListFilesResponse" } } } }, "400": { "description": "Bad request — the request was malformed or a parameter was invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Unauthorized — the API key is missing or invalid.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "403": { "description": "Forbidden — the API key lacks the required scope.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "404": { "description": "Not found — the requested resource does not exist or is not accessible.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Internal server error.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } } }, "tags": [ { "name": "AuthService", "description": "AuthService reports information about the API key making the request." }, { "name": "ExecutionService", "description": "ExecutionService provides access to workflow executions — runs of a\n bioinformatics workflow that process instrument data. Listing and reading\n execution metadata requires the \"executions:read\" scope; listing files and\n obtaining download credentials requires \"executions:download\"; retrieving\n logs requires \"executions:logs\"." }, { "name": "InstrumentService", "description": "InstrumentService provides access to instruments registered to the\n authenticated tenant. Requires the \"instruments:read\" scope." }, { "name": "RunService", "description": "RunService provides access to instrument runs, both sequencing and\n multiomics. Listing and reading run metadata requires the \"runs:read\"\n scope; listing run files and obtaining download credentials requires the\n \"runs:download\" scope." }, { "name": "StorageConnectionService", "description": "StorageConnectionService provides access to storage connections: their\n metadata (requires the \"storage:read\" scope) and the files within them\n (ListFiles / GetDownloadCredentials, which require the \"storage:download\"\n scope, narrowable to a specific connection or path prefix). Connections that\n are deleted, disabled, or queued for deletion are not returned." } ] }