Experimental Data Operations

Experimental Data Operations#

Warning

Experimental features may change or be removed in future versions. Use at your own risk.

Upload Datasets#

The upload_dataset feature allows you to create B-Fabric datasets from CSV files.

from pathlib import Path
from bfabric import Bfabric
from bfabric.experimental.upload_dataset import bfabric_save_csv2dataset

client = Bfabric.connect()

csv_file = Path("data/measurements.csv")
result = bfabric_save_csv2dataset(
    client=client,
    csv_file=csv_file,
    dataset_name="MyMeasurements",
    container_id=123,
    sep=",",
)

if result.is_success:
    print(f"Dataset created with ID: {result[0]['id']}")

Parameters#

  • client: Bfabric client instance

  • csv_file: Path to CSV file

  • dataset_name: Name for the new dataset

  • container_id: Container (project/order) ID to associate with

  • sep: CSV separator (default: comma)

  • check: Raise errors on failure (default: True)

Update Custom Attributes#

Update custom attributes on any entity by its URI.

from bfabric import Bfabric
from bfabric.entities.core.uri import EntityUri
from bfabric.experimental.update_custom_attributes import update_custom_attributes

client = Bfabric.connect()

custom_attrs = {"status": "processed", "qc_status": "passed"}
uri = EntityUri("https://fgcz-bfabric.uzh.ch/bfabric/sample/show.html?id=123")

result = update_custom_attributes(
    client=client,
    entity_uri=uri,
    custom_attributes=custom_attrs,
    replace=False,  # Merge with existing (default)
)

if result.is_success:
    print("Custom attributes updated")

Parameters#

  • client: Bfabric client instance

  • entity_uri: Entity URI of the entity to update

  • custom_attributes: Dictionary of custom attribute key-value pairs

  • replace: If True, replace all attributes. If False (default), merge with existing

Use Cases#

Workflow Status Tracking#

Track processing status across samples:

# Mark samples as processed
samples = reader.query(entity_type="sample", obj={"projectid": 123})

for uri, sample in samples.items():
    update_custom_attributes(
        client=client,
        entity_uri=uri,
        custom_attributes={"processing_status": "completed"},
    )

QC Result Annotation#

Add quality control results:

# Annotate samples with QC results
qc_results = {
    "qc_status": "passed",
    "qc_date": "2025-01-22",
    "qc_score": 0.95,
}

update_custom_attributes(
    client=client,
    entity_uri=sample_uri,
    custom_attributes=qc_results,
)

Limitations#

  • Custom attributes are B-Fabric specific and may not be available for all entity types

  • Attribute names must be valid B-Fabric custom attribute names

  • Values are stored as strings in B-Fabric

See Also#

Contents