benchling_sdk.services.v2.beta.v2_beta_dataset_service module¶

class V2BetaDatasetService¶

Bases: benchling_sdk.services.v2.base_service.BaseService

V2-Beta Datasets.

Datasets are Benchling objects that represent tabular data with typed columns and rows of data.

See https://benchling.com/api/v2-beta/reference#/Dataset

create(dataset: benchling_api_client.v2.beta.models.dataset_create.DatasetCreate) → benchling_api_client.v2.beta.models.dataset.Dataset¶

Create a dataset.

See https://benchling.com/api/v2-beta/reference#/Datasets/createDataset

create_from_bytes(dataset: benchling_api_client.v2.beta.models.dataset_create.DatasetCreate, input_bytes: Union[_io.BytesIO, bytes], timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATASET) → AsyncTaskLink¶

Create a dataset from bytes or BytesIO data.

Parameters

  • dataset – The DatasetCreate specification for the data. This must be provided, as it cannot be inferred from file names.

  • input_bytes – Data to upload as bytes or BytesIO

  • timeout_seconds – Extends the normal HTTP timeout settings since Dataset uploads can be large Use this to extend even further if streams are very large

Returns

An AsyncTaskLink that can be polled to know when the dataset has completed processing

Return type

AsyncTaskLink

create_from_file(file: Path, dataset: Optional[benchling_api_client.v2.beta.models.dataset_create.DatasetCreate] = None, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATASET) → AsyncTaskLink¶

Create a dataset from file data.

Parameters

  • file – A valid Path to an existing file containing the data to upload

  • dataset – The DatasetCreate specification for the data. If not provided, it will be inferred from the file name

  • timeout_seconds – Extends the normal HTTP timeout settings since Dataset uploads can be large Use this to extend even further if streams are very large

Returns

An AsyncTaskLink that can be polled to know when the dataset has completed processing

Return type

AsyncTaskLink

download_dataset_bytes(dataset: benchling_api_client.v2.beta.models.dataset.Dataset, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATASET) → List[_io.BytesIO]¶

Download dataset data to bytes.

Parameters

  • dataset – The dataset to download

  • timeout_seconds – Extends the normal HTTP timeout settings since Dataset uploads can be large Use this to extend even further if streams are very large

Returns

An ordered list of BytesIO streams corresponding to a manifest item in the dataset

Return type

List[BytesIO]

download_dataset_bytes_by_id(dataset_id: str, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATASET) → List[_io.BytesIO]¶

Download dataset data to files by dataset_id.

Fetches the dataset first, then downloads the files.

Parameters

  • dataset_id – The id of the dataset to download

  • timeout_seconds – Extends the normal HTTP timeout settings since Dataset uploads can be large Use this to extend even further if streams are very large

Returns

An ordered list of BytesIO streams corresponding to a manifest item in the dataset

Return type

List[BytesIO]

download_dataset_files(dataset: benchling_api_client.v2.beta.models.dataset.Dataset, destination_path: Optional[Path] = None, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATASET) → List[Path]¶

Download dataset data to files.

Parameters

  • dataset – The dataset to download

  • destination_path – A target directory to place the files. File names will be created based on the manifest item file names. If not specified, a temp directory will be created. The caller is responsible for deleting this directory.

  • timeout_seconds – Extends the normal HTTP timeout settings since Dataset uploads can be large Use this to extend even further if streams are very large

Returns

An ordered list of downloaded file paths corresponding to a manifest item in the dataset

Return type

List[Path]

download_dataset_files_by_id(dataset_id: str, destination_path: Optional[Path] = None, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATASET) → List[Path]¶

Download dataset data to files by dataset_id.

Fetches the dataset first, then downloads the files.

Parameters

  • dataset_id – The id of the dataset to download

  • destination_path – A target directory to place the files. File names will be created based on the manifest item file names. If not specified, a temp directory will be created. The caller is responsible for deleting this directory.

  • timeout_seconds – Extends the normal HTTP timeout settings since Dataset uploads can be large Use this to extend even further if streams are very large

Returns

An ordered list of downloaded file paths corresponding to a manifest item in the dataset

Return type

List[Path]

get_by_id(dataset_id: str) → benchling_api_client.v2.beta.models.dataset.Dataset¶

Get a dataset and URLs to download its data.

See https://benchling.com/api/v2-beta/reference#/Datasets/getDataset

update(dataset_id: str, dataset: benchling_api_client.v2.beta.models.dataset_update.DatasetUpdate) → AsyncTaskLink¶

Update a dataset.

See https://benchling.com/api/v2-beta/reference#/Datasets/patchDataset

upload_bytes(url: str, input_bytes: Union[_io.BytesIO, bytes], timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATASET) → None¶

Upload bytes to an existing dataset.

Parameters

  • url – The url provided by Benchling for uploading to the dataset

  • input_bytes – Data to upload as bytes or BytesIO

  • timeout_seconds – Extends the normal HTTP timeout settings since Dataset uploads can be large Use this to extend even further if streams are very large

upload_file(url: str, file: Path, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATASET) → None¶

Upload a file to an existing dataset.

Parameters

  • url – The url provided by Benchling for uploading to the dataset

  • file – A valid Path to an existing file containing the data to upload

  • timeout_seconds – Extends the normal HTTP timeout settings since Dataset uploads can be large Use this to extend even further if streams are very large