Configure the Output File Processor to Create New Entities

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Benchling has the ability to create and register entities using the lab automation output file processor. The functionality is convenient for use cases that require large numbers of entities to be created in one action.

Populated run and new entity


Process overview

  1. Create the entity schema you want to use in the Benchling registry if it doesn’t already exist.

  2. Create a Run Entity schema to process the output file and create the new entities.

  3. Create an output file with entity field information, one row for each new entity.

  4. Insert the run object into a Benchling notebook entry and create a new run.

  5. Upload the output file to the run and click Process. New entities are created and linked on the run.

Example output file




Text based information

Output files should be comma separated UTF-8 plain text format. Each row represents the schema field information for one new entity.

Example JSON configuration

Note: fields from the run schema can be accessed with a lookupConfig and used to populate fields of the new entities that are created.

"fields": [
"isMulti": false,
"type": "text",
"displayName": "Run field",
"name": "run_field",
"isRequired": false
"automationOutputFileConfigs": [
"entitySchemaInfo": {
"fields": {
"Date": {
"columnName": "Date",
"type": "DIRECT"
"Info": {
"columnName": "Info",
"type": "DIRECT"
"Run field": {
"lookupConfig": {
"lookupSteps": [
"type": "SCHEMA_FIELD",
"schemaField": "run_field"
"type": "LOOKUP"
"shouldReplaceExisting": false,
"schema": "ts_78oiNs0j",
"labelingStrategy": "DELETE_NAMES"
"name": "Entity creation",
"columnTypesByName": {
"delimiter": ",",
"fileExtension": "csv",
"tableType": "SAMPLE",
"spreadsheetProcessingLocale": "en-US"

For runs processing >=100k cells of entity creation information, File Queuing can be enabled to improve the convenience of uploading very large files into Benchling.

Benchling supports ingestion of localized numbers and dates. You can configure the Locale in your user settings. To learn more, visit Updating user locale

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