Help on module benchling_sdk.benchling in benchling_sdk:
NAME
benchling_sdk.benchling
CLASSES
builtins.object
Benchling
typing_extensions.Protocol(builtins.object)
BenchlingApiClientDecorator
class Benchling(builtins.object)
| Benchling(url: str, auth_method: benchling_api_client.benchling_client.AuthorizationMethod, base_path: Union[str, NoneType] = '/api/v2', retry_strategy: Union[benchling_sdk.helpers.retry_helpers.RetryStrategy, NoneType] = RetryStrategy(max_tries=5, backoff_factor=0.5, status_codes_to_retry=(<HTTPStatus.TOO_MANY_REQUESTS: 429>, <HTTPStatus.BAD_GATEWAY: 502>, <HTTPStatus.SERVICE_UNAVAILABLE: 503>, <HTTPStatus.GATEWAY_TIMEOUT: 504>)), client_decorator: Union[benchling_sdk.benchling.BenchlingApiClientDecorator, NoneType] = None)
|
| A 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://docs.benchling.com/docs/api/v2
|
| Methods defined here:
|
| __init__(self, url: str, auth_method: benchling_api_client.benchling_client.AuthorizationMethod, base_path: Union[str, NoneType] = '/api/v2', retry_strategy: Union[benchling_sdk.helpers.retry_helpers.RetryStrategy, NoneType] = RetryStrategy(max_tries=5, backoff_factor=0.5, status_codes_to_retry=(<HTTPStatus.TOO_MANY_REQUESTS: 429>, <HTTPStatus.BAD_GATEWAY: 502>, <HTTPStatus.SERVICE_UNAVAILABLE: 503>, <HTTPStatus.GATEWAY_TIMEOUT: 504>)), client_decorator: Union[benchling_sdk.benchling.BenchlingApiClientDecorator, NoneType] = None)
| Initialize Benchling.
|
| :param url: A server URL (host and optional port) including scheme such as https://benchling.com
| :param 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.
| :param 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
| :param retry_strategy: An optional retry strategy for retrying HTTP calls on failure. Setting to None
| will disable retries
| :param client_decorator: An optional function that accepts a BenchlingApiClient configured with
| default settings and mutates its state as desired
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
|
| aa_sequences
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/aa-sequences
|
| api
| 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.
|
| assay_results
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/assay-results
|
| assay_runs
| Assay Runs.
|
| Runs capture the details / parameters of a run that was performed. Results are usually nested under a run.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/assay-runs
|
| blobs
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/blobs
|
| boxes
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/boxes
|
| 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.
|
| containers
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/containers
|
| custom_entities
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/custom-entities
|
| dna_alignments
| DNA Alignments.
|
| A DNA alignment is a Benchling object representing an alignment of multiple DNA sequences.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/dna-alignments
|
| dna_sequences
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/dna-sequences
|
| dropdowns
| Dropdowns.
|
| Dropdowns are registry-wide enums. Use dropdowns to standardize on spelling and naming conventions, especially
| for important metadata like resistance markers.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/dropdowns
|
| entries
| Entries.
|
| Entries are rich text documents that allow you to capture all of your experimental data in one place.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/entries
|
| events
| Events.
|
| The Events system allows external services to subscribe to events that are triggered in Benchling (e.g. plasmid
| registration, request submission, etc).
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/events
|
| exports
| Exports.
|
| Export a Notebook Entry.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/exports
|
| folders
| Folders.
|
| Manage folder objects.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/folders
|
| inventory
| Inventory.
|
| Manage inventory wide objects.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/inventory
|
| lab_automation
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/lab-automation
|
| label_templates
| Label Templates.
|
| List label templates.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/label-templates
|
| locations
| Locations.
|
| Manage locations objects. Like all storage, every Location has a barcode that is unique across the registry.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/locations
|
| oligos
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/oligos
|
| plates
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/plates
|
| printers
| Printers.
|
| List printers.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/printers
|
| projects
| Projects.
|
| Manage project objects.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/projects
|
| registry
| Registry.
|
| Manage registry objects.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/registry
|
| requests
| Requests.
|
| Requests allow scientists and teams to collaborate around experimental assays and workflows.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/legacy-requests
|
| schemas
| 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
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/schemas
|
| tasks
| 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.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/tasks
|
| warehouse
| Warehouse.
|
| Manage warehouse credentials.
|
| See https://docs.benchling.com/docs/api/v2/benchling-api/warehouse
|
| ----------------------------------------------------------------------
| Data and other attributes defined here:
|
| __annotations__ = {'_aa_sequence_service': <class 'benchling_sdk.servi...
class BenchlingApiClientDecorator(typing_extensions.Protocol)
| BenchlingApiClientDecorator(*args, **kwds)
|
| For 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)
|
| Method resolution order:
| BenchlingApiClientDecorator
| typing_extensions.Protocol
| builtins.object
|
| Methods defined here:
|
| __call__(self, client: benchling_api_client.benchling_client.BenchlingApiClient) -> benchling_api_client.benchling_client.BenchlingApiClient
| Customize a BenchlingApiClient and return the updated client.
|
| :param client: The underlying API client with default configuration
| :type client: BenchlingApiClient
| :return: The updated client
| :rtype: BenchlingApiClient
|
| __init__ = _no_init(self, *args, **kwargs)
|
| __subclasshook__ = _proto_hook(other)
| # Set (or override) the protocol subclass hook.
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
|
| ----------------------------------------------------------------------
| Data and other attributes defined here:
|
| __abstractmethods__ = frozenset()
|
| __parameters__ = ()
|
| ----------------------------------------------------------------------
| Class methods inherited from typing_extensions.Protocol:
|
| __class_getitem__(params) from typing_extensions._ProtocolMeta
|
| __init_subclass__(*args, **kwargs) from typing_extensions._ProtocolMeta
| This method is called when a class is subclassed.
|
| The default implementation does nothing. It may be
| overridden to extend subclasses.
|
| ----------------------------------------------------------------------
| Static methods inherited from typing_extensions.Protocol:
|
| __new__(cls, *args, **kwds)
| Create and return a new object. See help(type) for accurate signature.
DATA
Optional = typing.Optional
