amazon-omics-tools 0.1.1

Tools for working with the Amazon Omics Service

Amazon Omics Tools

Tools for working with the Amazon Omics Service.

Using the Omics Transfer Manager

Basic Usage

The TransferManager class makes it easy to download files for an Omics reference or read set. By default the files are saved to the current directory, or you can specify a custom location with the directory parameter.

import boto3
from omics.transfer import ReferenceFileName, ReadSetFileName
from omics.transfer.manager import TransferManager
from omics.transfer.config import TransferConfig

REFERENCE_STORE_ID = "<my-reference-store-id>"
SEQUENCE_STORE_ID = "<my-sequence-store-id>"

client = boto3.client("omics")
manager = TransferManager(client)

# Download all files for a reference.
manager.download_reference(REFERENCE_STORE_ID, "<my-reference-id>")

# Download all files for a read set to a custom directory.
manager.download_read_set(SEQUENCE_STORE_ID, "<my-read-set-id>", "my-sequence-data")

Download specific files

Specific files can be downloaded via the download_reference_file and download_read_set_file methods. The client_fileobj parameter can be either the name of a local file to create for storing the data, or a TextIO or BinaryIO object that supports write methods.

# Download a specific reference file.
manager.download_reference_file(
    REFERENCE_STORE_ID,
    "<my-reference-id>",
    ReferenceFileName.INDEX
)

# Download a specific read set file with a custom filename.
manager.download_read_set_file(
    SEQUENCE_STORE_ID,
    "<my-read-set-id>",
    ReadSetFileName.INDEX,
    "my-sequence-data/read-set-index"
)

Subscribe to events

Transfer events: on_queued, on_progress, and on_done can be observed by defining a subclass of OmicsTransferSubscriber and passing in an object which can receive events.

class ProgressReporter(OmicsTransferSubscriber):
    def on_queued(self, **kwargs):
        future: OmicsTransferFuture = kwargs["future"]
        print(f"Download queued: {future.meta.call_args.fileobj}")

    def on_done(self, **kwargs):
        print("Download complete")

manager.download_read_set(SEQUENCE_STORE_ID, "<my-read-set-id>", subscribers=[ProgressReporter()])

Threads

Transfer operations use threads to implement concurrency. Thread use can be disabled by setting the use_threads attribute to False.

If thread use is disabled, transfer concurrency does not occur. Accordingly, the value of the max_request_concurrency attribute is ignored.

# Disable thread use/transfer concurrency
config = TransferConfig(use_threads=False)
manager = TransferManager(client, config)
manager.download_read_set(SEQUENCE_STORE_ID, "<my-read-set-id>")

Security

See CONTRIBUTING for more information.

License

This project is licensed under the Apache-2.0 License.