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
Create the entity schema you want to use in the Benchling registry if it doesn’t already exist
Create a run entity schema to process the output file and create the new entities
Create an output file with entity field information, one row for each new entity
Insert the run object into a Benchling notebook entry and create a new run
Upload the output file to the run and click the process button
New entities are created and linked on the run
Configuration details
Example output file
Date | Info |
2020-10-02T15:00:00Z | 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.
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": {
"isMulti":
false,
"lookupSteps": [
{
"type": "SCHEMA_FIELD",
"schemaField": "run_field"
}
]
},
"type": "LOOKUP"
}
},
"shouldReplaceExisting": false,
"schema": "ts_78oiNs0j",
"labelingStrategy": "DELETE_NAMES"
},
"name": "Entity creation",
"columnTypesByName": {
"Date": "SCHEMA_FIELD",
"Info": "SCHEMA_FIELD"
},
"delimiter": ","
,"fileExtension": "csv",
"tableType": "SAMPLE"
}
]
}
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.