CFDE Client

This is a client to interact with the Globus Automate Flows for CFDE use cases. Both a Python API and a CLI tool are available.

Installation

The CFDE Client requires Python 3.6 or later. To check which version of Python you have, run python --version. If you have both Python 2 and Python 3 installed, you may need to check with python3 --version. If this is the case, you will also need to use pip3 instead of pip below.

git clone https://github.com/fair-research/deriva-flow-client.git
cd deriva-flow-client
pip install -e .

Usage

This tool can ingest any of the following into DERIVA:

1. A directory to be formatted into a BDBag
2. A Git repository to be copied into a BDBag
3. A premade BDBag directory
4. A premade BDBag in an archive file

In all cases, the data must already be in CFDE TableSchema format, or the ingest may fail. See instructions here (link to docs pending).

Command line

There are four commands available: run, status, login, and logout. Use them as follows:

• cfde run DATA-PATH will ingest the data found at DATA-PATH into DERIVA. You can also specify the following options:

  • --catalog-id=CATALOG_ID will ingest into an existing catalog instead of creating a new catalog.
  • --output-dir=OUTPUT_DIR will copy the data in DATA-PATH, if it is a directory, to the location you specify, which must not exist and must not be inside DATA-PATH. The resulting BDBag will be named after the output directory. If not specified, the BDBag will be created in-place in DATA_PATH if necessary.
  • --delete-dir will trigger deletion of the output-dir after processing is complete. If you didn't specify output-dir, this option has no effect.
  • --ignore-git will prevent the client from overwriting output-dir and delete-dir to handle Git repositories.

• cfde status will check the status of a Flow instance. By default, the last run Flow is used, but if you want to check a previous Flow you can provide one or both of the following options:

  • --flow-id=ID is the ID of the Flow itself (NOT a specific instance of the Flow).
  • --flow-instance-id=ID is the ID of the particular instance/invocation of the Flow you want to check.

• cfde login will start the login process. If you have tokens saved from a previous login, this command will validate those tokens and only re-authenticate you if they are expired. It is not necessary to run this command before run or status, because those commands will also authenticate you if needed.

• cfde logout will log you out and revoke any valid cached tokens.

Python API

The CfdeClient class, once instantiated, has the following methods:

• start_deriva_flow(self, data_path, catalog_id=None, output_dir=None, delete_dir=False, **kwargs)
• check_status(self, flow_id=None, flow_instance_id=None, raw=False)
• logout(self)

The arguments operate in the same fashion as the CLI options, and are documented in detail in the method docstrings.