benchling_sdk.benchling module¶
Provides the Benchling class, which is the main interface for accessing Benchling’s API functionality.
- class Benchling¶
Bases:
objectA facade for interactions with the Benchling platform.
Methods are organized into namespaces which generally correspond to Resources in Benchling’s public API doc.
See https://benchling.com/api/reference
- __init__(url: str, auth_method: benchling_api_client.v2.benchling_client.AuthorizationMethod, base_path: Optional[str] = _DEFAULT_BASE_PATH, retry_strategy: Optional[RetryStrategy] = _DEFAULT_RETRY_STRATEGY, client_decorator: Optional[BenchlingApiClientDecorator] = None, httpx_client: Optional[httpx.Client] = None)¶
Initialize Benchling.
- Parameters
url – A server URL (host and optional port) including scheme such as https://benchling.com
auth_method – A provider of an HTTP Authorization header for usage with the Benchling API. Pass an instance of benchling_sdk.auth.api_key_auth.ApiKeyAuth with a valid Benchling API token for authentication and authorization through HTTP Basic Authentication, or a client_id and client_secret pair with benchling_sdk.auth.client_credentials_oauth2.ClientCredentialsOAuth2 for authentication and authorization through OAuth2 client_credentials Bearer token flow.
base_path – If provided, will append to the host. Otherwise, assumes the V2 API. This is a workaround until the generated client supports the servers block. See BNCH-15422
retry_strategy – An optional retry strategy for retrying HTTP calls on failure. Setting to None will disable retries
client_decorator – An optional function that accepts a BenchlingApiClient configured with default settings and mutates its state as desired
httpx_client – An optional httpx Client which will be used to execute HTTP calls. The Client can be used to modify the behavior of the HTTP calls made to Benchling through means such as adding proxies and certificates or introducing retry logic for transport-level errors.
- property aa_sequences: AaSequenceService¶
AA Sequences.
AA Sequences are the working units of cells that make everything run (they help make structures, catalyze reactions and allow for signaling - a kind of internal cell communication). On Benchling, these are comprised of a string of amino acids and collections of other attributes, such as annotations.
- property api: ApiService¶
Make custom API calls with the underlying BenchlingApiClient.
A common use case for this is making calls to API endpoints which may not yet be supported in the current SDK release. It’s capable of making more “generic” calls utilizing our authorization scheme, as well as supporting some simple serialization and deserialization for custom models.
- property apps: AppService¶
Apps.
Apps provide a framework for you to customize your teams’ experiences on Benchling with custom applications.
See https://benchling.com/api/reference#/Apps and https://docs.benchling.com/docs/getting-started-benchling-apps
- property assay_results: AssayResultService¶
Assay Results.
Results represent the output of assays that have been performed. You can customize the schemas of results to fit your needs. Results can link to runs, batches, and other types.
- property assay_runs: AssayRunService¶
Assay Runs.
Runs capture the details / parameters of a run that was performed. Results are usually nested under a run.
- property blobs: BlobService¶
Blobs.
Blobs are opaque files that can be linked to other items in Benchling, like assay runs or results. For example, you can upload a blob, then upload an assay result that links to that blob by ID. The blob will then appear as part of the assay result in the Benchling web UI.
- property boxes: BoxService¶
Boxes.
Boxes are a structured storage type, consisting of a grid of positions that can each hold one container. Unlike locations, there are a maximum number of containers that a box can hold (one per position).
Boxes are all associated with schemas, which define the type of the box (e.g. “10x10 Cryo Box”) along with the fields that are tracked and the dimensions of the box.
Like all storage, every Box has a barcode that is unique across the registry.
- property client: benchling_api_client.v2.client.Client¶
Provide access to the underlying generated Benchling Client.
Should generally not be used except for advanced use cases which may not be well supported by the SDK itself.
- property codon_usage_tables: CodonUsageTableService¶
Codon Usage Tables.
Benchling curates codon usage data for a variety of organisms to support operations such as Codon Optimization and Back Translation.
See https://benchling.com/api/reference#/Codon%20Usage%20Tables
- property containers: ContainerService¶
Containers.
Containers are the backbone of sample management in Benchling. They represent physical containers, such as tubes or wells, that hold quantities of biological samples (represented by the batches inside the container). The container itself tracks its total volume, and the concentration of every batch inside of it.
Containers are all associated with schemas, which define the type of the container (e.g. “Tube”) along with the fields that are tracked.
Like all storage, every container has a barcode that is unique across the registry.
- property custom_entities: CustomEntityService¶
Custom Entities.
Benchling supports custom entities for biological entities that are neither sequences or proteins. Custom entities must have an entity schema set and can have both schema fields and custom fields.
- property custom_notations: CustomNotationService¶
Custom Notations.
Benchling allows users to configure their own fully-custom string representation formats for import/export of nucleotide sequences (including chemical modifications).
- property dna_alignments: DnaAlignmentsService¶
DNA Alignments.
A DNA alignment is a Benchling object representing an alignment of multiple DNA sequences.
- property dna_oligos: DnaOligoService¶
DNA Oligos.
DNA Oligos are short linear DNA sequences that can be attached as primers to full DNA sequences. Just like other entities, they support schemas, tags, and aliases.
- property dna_sequences: DnaSequenceService¶
DNA Sequences.
DNA sequences are the bread and butter of the Benchling Molecular Biology suite. On Benchling, these are comprised of a string of nucleotides and collections of other attributes, such as annotations and primers.
- property dropdowns: DropdownService¶
Dropdowns.
Dropdowns are registry-wide enums. Use dropdowns to standardize on spelling and naming conventions, especially for important metadata like resistance markers.
- property entities: EntityService¶
Entities.
Entities include DNA and AA sequences, oligos, molecules, custom entities, and other biological objects in Benchling. Entities support schemas, tags, and aliases, and can be registered.
- property entries: EntryService¶
Entries.
Entries are rich text documents that allow you to capture all of your experimental data in one place.
- property enzymes: EnzymeService¶
Enzymes.
Restriction enzymes are curated by Benchling for operations such as Digests and Codon Optimization.
- property events: EventService¶
Events.
The Events system allows external services to subscribe to events that are triggered in Benchling (e.g. plasmid registration, request submission, etc).
- property exports: ExportService¶
Exports.
Export a Notebook Entry.
- property feature_libraries: FeatureLibraryService¶
Feature Libraries.
Feature Libraries are collections of shared canonical patterns that can be used to generate annotations on matching regions of DNA Sequences or AA Sequences.
See https://benchling.com/api/reference#/Feature%20Libraries
- property folders: FolderService¶
Folders.
Manage folder objects.
- property instrument_queries: InstrumentQueryService¶
Instrument Queries.
Instrument Queries are used to query the instrument service.
See https://benchling.com/api/reference#/Instrument%20Queries
- property inventory: InventoryService¶
Inventory.
Manage inventory wide objects.
- property lab_automation: LabAutomationService¶
Lab Automation.
Lab Automation endpoints support integration with lab instruments, and liquid handlers to create samples or results, and capture transfers between containers at scale.
- property label_templates: LabelTemplateService¶
Label Templates.
List label templates.
- property locations: LocationService¶
Locations.
Manage locations objects. Like all storage, every Location has a barcode that is unique across the registry.
- property mixtures: MixtureService¶
Mixtures.
Mixtures are solutions comprised of multiple ingredients where the exact quantities of each ingredient are important to track. Each ingredient is uniquely identified by its component entity.
- property molecules: MoleculeService¶
Molecules.
Molecules are groups of atoms held together by bonds, representing entities smaller than DNA Sequences and AA Sequences. Just like other entities, they support schemas, tags, and aliases.
- property monomers: MonomerService¶
Monomers.
Monomers are chemical building blocks with specified structures used to compose modified nucleotides. Note that monomer write endpoints require tenant admin permissions.
- property nucleotide_alignments: NucleotideAlignmentsService¶
Nucleotide Alignments.
A Nucleotide Alignment is a Benchling object representing an alignment of multiple DNA and/or RNA sequences.
See https://benchling.com/api/reference#/Nucleotide%20Alignments
- property oligos: OligoService¶
Oligos.
Oligos are short linear DNA sequences that can be attached as primers to full DNA sequences. Just like other entities, they support schemas, tags, and aliases.
Please migrate to the corresponding DNA Oligos endpoints so that we can support RNA Oligos.
- property organizations: OrganizationService¶
Organizations.
View organization objects.
- property plates: PlateService¶
Plates.
Plates are a structured storage type, grids of wells that each function like containers. Plates come in two types: a traditional “fixed” type, where the wells cannot move, and a “matrix” type. A matrix plate has similar functionality to a box, where the containers inside can be moved around and removed altogether.
Plates are all associated with schemas, which define the type of the plate (e.g. “96 Well Plate”) along with the fields that are tracked, the dimensions of the plate, and whether or not the plate is a matrix plate or a traditional well plate.
Like all storage, every Plate has a barcode that is unique across the registry.
- property printers: PrinterService¶
Printers.
List printers.
- property projects: ProjectService¶
Projects.
Manage project objects.
- property registry: RegistryService¶
Registry.
Manage registry objects.
- property requests: RequestService¶
Requests.
Requests allow scientists and teams to collaborate around experimental assays and workflows.
- property rna_oligos: RnaOligoService¶
RNA Oligos.
RNA Oligos are short linear RNA sequences that can be attached as primers to full DNA sequences. Just like other entities, they support schemas, tags, and aliases.
- property rna_sequences: RnaSequenceService¶
RNA Sequences.
Chains of linear, single stranded RNA that support most capabilities and attributes of DNA Sequences.
- property schemas: SchemaService¶
Schemas.
Schemas represent custom configuration of objects in Benchling. See https://docs.benchling.com/docs/schemas in our documentation on how Schemas impact our developers
- property tasks: TaskService¶
Tasks.
Endpoints that perform expensive computations launch long-running tasks. These endpoints return the task ID (a UUID) in the response body.
After launching a task, periodically invoke the Get a task endpoint with the task UUID (e.g., every 10 seconds), until the status is no longer RUNNING.
You can access a task for up to 30 minutes after its completion, after which its data will no longer be available.
- property teams: TeamService¶
Teams.
View team objects.
- property users: UserService¶
Benchling users.
- property warehouse: WarehouseService¶
Warehouse.
Manage warehouse credentials.
- property workflow_flowchart_config_versions: WorkflowFlowchartConfigVersionService¶
Workflow Flowchart Config Versions.
Workflow flowchart config versions are versioned graphs of flowchart configurations.
See https://benchling.com/api/reference#/Workflow%20Flowchart%20Config%20Versions
- property workflow_flowcharts: WorkflowFlowchartService¶
Workflow Flowcharts.
Workflow flowcharts represent the nodes and edges that a flowchart is comprised of.
See https://benchling.com/api/reference#/Workflow%20Flowcharts
- property workflow_outputs: WorkflowOutputService¶
Workflow Outputs.
Workflow outputs are outputs of a workflow task.
- property workflow_task_groups: WorkflowTaskGroupService¶
Workflow Tasks Groups.
Workflow task groups are groups of workflow tasks of the same schema.
See https://benchling.com/api/reference#/Workflow%20Task%20Groups
- property workflow_tasks: WorkflowTaskService¶
Workflow Tasks.
Workflow tasks encapsulate a single unit of work.
- class BenchlingApiClientDecorator¶
Bases:
ProtocolFor customizing a BenchlingApiClient client, which gives access to the underlying HTTPX layer.
Functions implementing this Protocol will receive the default BenchlingApiClient and may mutate specific attributes, returning the updated BenchlingApiClient.
A common use case for this is extending the default HTTP timeout:
def higher_timeout_client(client: BenchlingApiClient) -> BenchlingApiClient: return client.with_timeout(180)
- __init__(*args, **kwargs)¶