openapi: 3.2.0 info: license: name: Apache 2.0 url: http://www.apache.org/licenses/LICENSE-2.0.html title: Benchling Analysis API version: 2.0.0 description: Operations for Analysis servers: - url: /api/v3 security: - oAuth: [] - basicApiKeyAuth: [] tags: - description: Operations for Analysis name: Analysis x-bnch-organization: Benchling paths: /analysis/items: get: description: List Analysis items. operationId: Analysis.List parameters: - $ref: '#/components/parameters/archiveReason.anyOf' - $ref: '#/components/parameters/archived.anyOf' - $ref: '#/components/parameters/createdAt.gt' - $ref: '#/components/parameters/createdAt.gte' - $ref: '#/components/parameters/createdAt.lt' - $ref: '#/components/parameters/createdAt.lte' - $ref: '#/components/parameters/id.anyOf' - $ref: '#/components/parameters/modifiedAt.gt' - $ref: '#/components/parameters/modifiedAt.gte' - $ref: '#/components/parameters/modifiedAt.lt' - $ref: '#/components/parameters/modifiedAt.lte' - $ref: '#/components/parameters/name.anyOf' - $ref: '#/components/parameters/name.anyOf.caseSensitive' - $ref: '#/components/parameters/nextToken' - $ref: '#/components/parameters/omit' - $ref: '#/components/parameters/pageSize' - $ref: '#/components/parameters/returning' - description: 'Method by which to order results. Valid sorts are: createdAt (created time, oldest first) and modifiedAt (modified time, oldest first). Use :asc or :desc to specify ascending or descending order. Default is modifiedAt:desc.' in: query name: sort schema: default: modifiedAt:desc enum: - createdAt:asc - createdAt:desc - modifiedAt:asc - modifiedAt:desc type: string - description: Set to true to access beta operations via /api/v3. in: header name: EARLY-ACCESS required: false schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/AnalysisPaginatedList' description: OK headers: {} '400': $ref: '#/components/responses/BadRequest' '403': $ref: '#/components/responses/Forbidden' '404': $ref: '#/components/responses/NotFound' '429': $ref: '#/components/responses/TooManyRequests' '500': $ref: '#/components/responses/InternalServerError' summary: List Analysis items tags: - Analysis x-bnch-rate-limit-tier: 4 /analysis/{analysis_id}: get: description: Get a single Analysis by ID. operationId: Analysis.Get parameters: - description: ID of the Analysis. in: path name: analysis_id required: true schema: type: string - $ref: '#/components/parameters/returning' - $ref: '#/components/parameters/omit' - description: Set to true to access beta operations via /api/v3. in: header name: EARLY-ACCESS required: false schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/Analysis' description: OK headers: {} '400': $ref: '#/components/responses/BadRequest' '403': $ref: '#/components/responses/Forbidden' '404': $ref: '#/components/responses/NotFound' '429': $ref: '#/components/responses/TooManyRequests' '500': $ref: '#/components/responses/InternalServerError' summary: Get Analysis by ID tags: - Analysis x-bnch-rate-limit-tier: 5 /analysis/{analysis_id}/steps/items: get: description: List PipelineStep items. operationId: Analysis.steps.List parameters: - description: ID of the Analysis. in: path name: analysis_id required: true schema: type: string - description: Set to true to access beta operations via /api/v3. in: header name: EARLY-ACCESS required: false schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/PipelineStepUnpaginatedList' description: OK headers: {} '400': $ref: '#/components/responses/BadRequest' '403': $ref: '#/components/responses/Forbidden' '404': $ref: '#/components/responses/NotFound' '429': $ref: '#/components/responses/TooManyRequests' '500': $ref: '#/components/responses/InternalServerError' summary: List PipelineStep items tags: - Analysis x-bnch-rate-limit-tier: 4 components: schemas: PipelineStep: description: 'Represents a single operation node within a Pipeline''s directed acyclic graph (DAG). Each step performs a specific transformation determined by its stepType (see `PipelineStepType`), with configuration options stored in the config field. Steps receive data through inputStepDatas and produce results via outputStepDatas (see `PipelineStepData`). The incomingEdges and outgoingEdges (see `PipelineStepEdge`) define the data flow connections to other steps. Execution state is tracked through statusCode and statusMessage. Steps support provenance tracking through the provenanceUri field for tracing data lineage.' properties: __typename: type: string config: type: - 'null' - object createdAt: format: datetime type: string id: type: string inputStepDatas: format: uri type: string modifiedAt: format: datetime type: string outputStepDatas: format: uri type: string pipeline: $ref: '#/components/schemas/PipelineRef' statusCode: enum: - AI_PROPOSED - BLOCKED - FAILED - HALTED - RUNNING - SUCCEEDED - WAITING type: string statusMessage: type: - 'null' - string stepType: enum: - AGGREGATE_DATASET - AUTOFILL_ANTIBODY_ELEMENT_SUBELEMENTS - ANNOTATE_ANTIBODY_INPUTS - ANOVA - APPLY_COLUMN_MAPPING - BIN_DATA - BOLTZ2 - BOLTZGEN - BOLTZGEN_SUCCESS - BULK_IMPORT - CHAI1 - CHART_VIEW - COMPUTED_COLUMN - CONCATENATE_ANTIBODY_COMPONENT_DOMAINS_TO_CHAINS - CONNECTION_DATA_DATASET - CONVERT_ASM_TO_CSV - CONVERT_FILE_TO_DATASET_WITH_DATA_ENTRY_ASSISTANT - CONVERT_JSON_TO_DATASET - CONVERT_OPENFOLD2_OUTPUT - CONVERT_OPENFOLD3_OUTPUT - CONVERT_TO_ASM - CREATE_DATASET_FROM_FILE - CREATE_ENTITIES - CREATE_METERING_USAGE_CHART - CREATE_PROCEDURE_DATASET - DATASET_VIEW - DATA_CATALOG_DATASET - DATA_CATALOG_FILE - DATA_CATALOG_FILES - DEFINE_TEMPLATE_VARIABLES - EXPERIMENT_OPTIMIZATION_BOOTSTRAP - EXPERIMENT_OPTIMIZATION_CLEAN_DATA - EXPERIMENT_OPTIMIZATION_EXPLANATION - EXPERIMENT_OPTIMIZATION_GENERATE_SEARCH_SPACE - EXPERIMENT_OPTIMIZATION_POSTERIOR_SUMMARY - EXPERIMENT_OPTIMIZATION_RECOMMENDATION - EXPERIMENT_OPTIMIZATION_TRAINING - EXPLORATORY_DATA_ANALYSIS - EXPORT_DATA_CATALOG_DATASET - EXPORT_DATA_CATALOG_FILE - EXTRACT_DATA_FRAME_VALUE - EXTRACT_OR_REMOVE_LINES - FILL_PLATE - FILTER_DATASET - FIND_AND_REPLACE - FLAG_ROWS - FORMAT_COLUMNS - GENERATE_ANALYSIS_VIEW_URL - GENERATE_BOLTZGEN_YAML - GENERATE_BOLTZ_YAML - GENERATE_FASTA - GENERATE_MODEL_RUN_INPUT - GENERATE_OPENFOLD2_JSON - GENERATE_OPENFOLD3_JSON - HIDE_COLUMNS - IMPORT_PLATES - IMPORT_SCRATCH_FILE - INITIALIZE_DATASET - INSERT_RESULT_URL_IN_DOCUMENT - INTERPOLATE_MARKDOWN - JOIN - LAYOUT - LEGACY_DATA_IMPORT_ENTRY_CREATION - LEGACY_DATA_IMPORT_INITIATION - LEGACY_DATA_IMPORT_TRANSCRIPTION - LOOK_UP - MAP_COLUMNS - MAP_JSON_TO_DATASETS_AND_FILES - MODEL_RUN_INFERENCE - MOVE_INVENTORY_PLATES - COMPUTE_NDC_ENTITY_MERGED_COLUMNS - NDC_COMBINE_DOMAINS_TO_VARIABLE_PAIRS - NDC_EXPAND_VARIABLE_PAIRS_TO_DOMAINS - NDC_REFERENCE_EXISTING_COMPONENTS - NOTEBOOK_TABLE_DATASET - OPENFOLD2 - OPENFOLD3 - PARAMETER_OPTIMIZATION_CONFIGURATION - PARAMETER_OPTIMIZATION_DATASET_CONFIGURATION - PARAMETER_OPTIMIZATION_MODELING - PARAMETER_OPTIMIZATION_PREDICTION - PIVOT_DATASET - PLATE_SCHEMA_DATASET - PLATES_TO_DATASETS - POSTPROCESS_MODEL_RUN - PROCEDURE_RUN_DATA_FRAMES - PROMOTE_DATASET - REGISTRY_SCHEMA_DATASET - REGISTER_PLATES_IN_INVENTORY - REGRESSION - REGRESSION_INTERPOLATION - RENAME_COLUMNS - REORDER_COLUMNS - RETYPE_COLUMNS - RUN_HAMILTON_METHOD - RUN_HIGHRES_PROTOCOL - RUN_OPENTRONS_PROTOCOL - SAVE_STRUCTURE_PREDICTION - SAVE_TO_RESULTS - SEND_TO_CONNECTION - SEND_TO_DOCUMENT - SEND_USER_NOTIFICATION - SORT_COLUMNS - STATIC_TEMPLATE_INPUT_TABLE - TABLE_VIEW - TEMPLATE_INPUT - TEST_ALL_CONFIGS - THIRD_PARTY - TRANSFER_PLATES - TRANSFORM_PROTEIN_BULK_INGEST_OUTPUT_TO_DATASET - TRANSLATE_ANTIBODY_COMPONENT_DNA_TO_AA - T_TEST - UNION_DATASETS - UNPIVOT_DATASET - UPDATE_ENTITIES - UPLOAD_CSV_DATASET - USER_DEFINED_FUNCTION - GENERATE_NDC_ERROR_CSV - VALIDATE_AND_TRANSFORM_ANTIBODY_INPUTS - VARIABLE_TEMPLATE_INPUT_TABLE - WAREHOUSE_SQL_DATASET - WINDOW_FUNCTIONS type: string stepVersion: type: integer type: object AnalysisPaginatedList: additionalProperties: false properties: items: items: $ref: '#/components/schemas/Analysis' type: array nextToken: type: string type: object PipelineStepUnpaginatedList: additionalProperties: false properties: items: items: $ref: '#/components/schemas/PipelineStep' type: array type: object InternalServerError: properties: detail: type: - 'null' - string - object errorId: type: string instance: type: string status: type: integer title: type: - 'null' - string type: type: string required: - type - title - detail - status - instance type: object PipelineRef: properties: __typename: type: string id: format: api_id type: string type: object PrincipalRef: properties: __typename: type: string id: format: api_id type: string type: object FolderRef: properties: __typename: type: string id: format: api_id type: string type: object Analysis: properties: __typename: type: string archiveReason: type: - 'null' - string archived: type: boolean createdAt: format: datetime type: string creator: $ref: '#/components/schemas/PrincipalRef' description: type: - 'null' - string folder: $ref: '#/components/schemas/FolderRef' id: type: string modifiedAt: format: datetime type: string name: type: string statusCode: enum: - AI_PROPOSED - BLOCKED - FAILED - HALTED - RUNNING - SUCCEEDED - WAITING type: string steps: format: uri type: string webUrl: type: string type: object GeneralError: properties: detail: type: - 'null' - string - object instance: type: string status: type: integer title: type: - 'null' - string type: type: string required: - type - title - detail - status - instance type: object parameters: pageSize: description: Number of results to return. Defaults to 50, maximum of 100. in: query name: pageSize schema: type: integer createdAt.gte: description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created at or after the specified time. e.g. >= 2017-04-30. in: query name: createdAt.gte schema: format: datetime type: string modifiedAt.gt: description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified after the specified time. e.g. > 2017-04-30. in: query name: modifiedAt.gt schema: format: datetime type: string modifiedAt.lte: description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified at or before the specified time. e.g. <= 2017-04-30. in: query name: modifiedAt.lte schema: format: datetime type: string id.anyOf: description: Restricts results to those matching any of the specified IDs. Comma-separated list. explode: false in: query name: id.anyOf schema: items: type: string maxItems: 100 type: array omit: description: Comma-separated list of top-level fields to omit from each returned item. Cannot overlap with returning. explode: false in: query name: omit schema: items: type: string type: array modifiedAt.lt: description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified before the specified time. e.g. < 2017-04-30. in: query name: modifiedAt.lt schema: format: datetime type: string createdAt.gt: description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created after the specified time. e.g. > 2017-04-30. in: query name: createdAt.gt schema: format: datetime type: string createdAt.lt: description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created before the specified time. e.g. < 2017-04-30. in: query name: createdAt.lt schema: format: datetime type: string archiveReason.anyOf: description: Restricts items to those with any of the specified archive reasons. Use "NOT_ARCHIVED" to filter for unarchived items. Use "ANY_ARCHIVED" to filter for archived items regardless of reason. Use "ANY_ARCHIVED_OR_NOT_ARCHIVED" to return items for both archived and unarchived. Comma-separated list. explode: false in: query name: archiveReason.anyOf schema: items: type: string maxItems: 10 type: array returning: description: Comma-separated list of top-level fields to include in each returned item. Cannot overlap with omit. explode: false in: query name: returning schema: items: type: string type: array archived.anyOf: description: If true, returns archived items. If false, returns unarchived items. If both true and false, returns archived and unarchived items. Comma-separated list. explode: false in: query name: archived.anyOf schema: items: type: boolean maxItems: 2 type: array nextToken: description: Token for pagination in: query name: nextToken schema: type: string name.anyOf: description: Restricts results to those that match any of the specified names. Case insensitive. Warning - this filter can be non-performant due to case insensitivity. Ensure only one name filter is used at a time. Comma-separated list. explode: false in: query name: name.anyOf schema: items: type: string maxItems: 100 type: array name.anyOf.caseSensitive: description: Restricts results to those that match any of the specified names. Case sensitive. Ensure only one name filter is used at a time. Comma-separated list. explode: false in: query name: name.anyOf.caseSensitive schema: items: type: string maxItems: 100 type: array modifiedAt.gte: description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified at or after the specified time. e.g. >= 2017-04-30. in: query name: modifiedAt.gte schema: format: datetime type: string createdAt.lte: description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created at or before the specified time. e.g. <= 2017-04-30. in: query name: createdAt.lte schema: format: datetime type: string responses: NotFound: content: application/problem+json: schema: $ref: '#/components/schemas/GeneralError' description: Not Found TooManyRequests: content: application/problem+json: schema: $ref: '#/components/schemas/GeneralError' description: Too Many Requests BadRequest: content: application/problem+json: schema: $ref: '#/components/schemas/GeneralError' description: Bad Request Forbidden: content: application/problem+json: schema: $ref: '#/components/schemas/GeneralError' description: Forbidden InternalServerError: content: application/problem+json: schema: $ref: '#/components/schemas/InternalServerError' description: Internal Server Error securitySchemes: basicApiKeyAuth: description: Use issued API key for standard access to the API scheme: basic type: http basicClientIdSecretAuth: description: Auth used as part of client credentials OAuth flow prior to receiving a bearer token. scheme: basic type: http oAuth: description: OAuth2 Client Credentials flow intended for service access flows: clientCredentials: scopes: {} tokenUrl: /oauth/token type: oauth2