benchlingapi

BenchlingAPI

The (unofficial) python API wrapper for Benchling. For more information, see documentation at https://klavinslab.github.io/benchling-api/index.

Installation

pip install benchlingapi -U

Getting Started

Initialize a session using your Benchling-provided API key:

from benchlingapi import Session
session = Session("your_secret_benchling_api_key")

From there, you can access various models:

session.DNASequence
session.AASequence
session.Oligo
session.Folder
session.Project
session.Registry
session.Translation
session.EntitySchema
session.Batch
session.CustomEntity

Finding models:

# get one model
dna = session.DNASequence.one()

# find a specific model by its id
dna = session.DNASequence.find('sdg_4tg23')

# get the last 50 amino acids
proteins = session.AASequence.last(50)

# get a registry by name
registry = session.Registry.find_by_name("Klavins Lab Registry")

Updating models:

dna = session.DNASequence.one()
dna.name = "My new name"
dna.bases = "AGGTAGGGTAGGGCCAGAGA"

# update the sequence on the server
dna.update()

Saving new models:

folder = session.Folder.find_by_name("My API Folder")
dna = session.DNASequence(
    name = 'my new dna',
    bases = 'AGGTAGGATGGCCA',
    folder_id = folder.id,
    is_circular = False
)

# save the dna to your Benchling account
dna.save()

Registering models to your registry:

dna.set_schema("My DNA Schema")
dna.register()

See the documentation for more information: https://klavinslab.github.io/benchling-api/index

Testing

Testing is done using pytest. Tests will create live requests to a Benchling account. Since testing is done live, a Benchling account will need to be setup along with testing data.

To run tests, you must have a Benchling Account with an API key. Tests require a file in 'tests/secrets/config.json' with the following format:

{
  "credentials": {
    "api_key": "asdahhjwrthsdfgadfadfgadadsfa"
  },
  "sharelinks": [
    "https://benchling.com/s/seq-asdfadsfaee"
  ],
  "project": {
    "name": "API"
  },
  "trash_folder": {
    "name": "API_Trash"
  },
  "inventory_folder": {
    "name": "API_Inventory"
  }
}

On the Benchling side of things, in the account liked to the credentials["api_key"], you must have a project corresponding to the project["name"] value above. Within this project, you should have two folder corresponding to the trash_folder and inventory_folder values above. Additionally, you should have at least one example of an AminoAcid, DNASequence, CustomEntity, and Oligo stored within your inventory_folder. Tests will copy the examples from the inventory_folder for downstream tests. After the tests, conclude, inventory in the trash_folder will get archived.

Happy Cloning!