A Python 3.9+ library for the Cirro platform.

You can install Cirro using pip:

pip install cirro

or you can install the main branch of the repo by running:

pip install git+https://github.com/CirroBio/Cirro-client.git

Upon first use, the Cirro client will ask if you would like to save your login information and give you a link to authenticate through the web browser.

If you need to change your credentials after this point, and you've opted to save your login, please see the clearing saved login section.

Usage: cirro download [OPTIONS]

  Download dataset files

Options:
  --project TEXT         Name or ID of the project
  --dataset TEXT         ID of the dataset
  --data-directory TEXT  Directory to store the files
  -i, --interactive      Gather arguments interactively
  --help                 Show this message and exit.

Usage: cirro upload [OPTIONS]

  Upload and create a dataset

Options:
  --name TEXT             Name of the dataset
  --description TEXT      Description of the dataset (optional)
  --project TEXT          Name or ID of the project
  --process TEXT          Name or ID of the ingest process
  --data-directory TEXT   Directory you wish to upload
  -i, --interactive       Gather arguments interactively
  --help                  Show this message and exit.

Usage: cirro list-datasets [OPTIONS]

  List available datasets

Options:
  --project TEXT         ID of the project
  -i, --interactive      Gather arguments interactively
  --help                 Show this message and exit.

When running a command, you can specify the --interactive flag to gather the command arguments interactively.

Example:

$ cirro upload --interactive
? What project is this dataset associated with?  Test project
? Enter the full path of the data directory  /shared/biodata/test
? Please confirm that you wish to upload 20 files (0.630 GB)  Yes
? What type of files?  Illumina Sequencing Run
? What is the name of this dataset?  test
? Enter a description of the dataset (optional)

See the following set of Jupyter notebooks that contain examples on the following topics:

View the API documentation for this library here.

The cirro configure command creates a file in CIRRO_HOME called config.ini.

You can set the base_url property in the config file rather than using the environment variable.

The transfer_max_retries configuration property specifies the maximum number of times to attempt uploading a file to Cirro in the event of a transfer failure. When uploading files to Cirro, network issues or temporary outages can occasionally cause a transfer to fail. It will pause for an increasing amount of time for each retry attempt.

The enable_additional_checksums property manages the utilization of SHA-256 hashing for enhanced data integrity. This feature computes the SHA-256 hash of a file during the upload process, and subsequently cross-validates it with the server upon completion. When retrieving files, it ensures that the hash received matches the server's stored hash. The default hashing algorithm for files is MD5. In many cases, MD5 is sufficient to ensure data integrity upon upload.

[General]
base_url = cirro.bio
transfer_max_retries = 15
enable_additional_checksums = true

You can clear your saved login information by removing the ~/.cirro/token.dat file from your system or by running cirro configure and selecting No when it asks if you'd like to save your login information.