aind-data-transfer-lite

Getting Started

Who is this for?

You want to upload data to AIND's Cloud Storage platform on AWS.

Prerequisites

Authentication for write permissions to aind-open-data bucket. Please reach out to AIND Scientific Computing for access.

Installation

Install directly from PyPI. We recommend installing into a virtual environment or conda environment.

pip install aind-data-transfer-lite

Usage

You can interact with AIND Data Transfer Lite in two ways:

1. Launch the GUI window for visual interaction.
2. Run Python scripts or the command-line interface to perform data uploads programmatically.

Launching the UI

• Ensure dependencies are installed.

• Either:

  • Open the file src/aind_data_transfer_lite/ui.py in VS Code and click "Run" in the upper right-hand corner.

  • Or run the following in the terminal:

    python -m aind_data_transfer_lite.ui

• You should see a window titled "AIND Data Transfer Lite" appear.

Example Python Script

from pathlib import Path
import os
from aind_data_transfer_lite.models import JobSettings
from aind_data_transfer_lite.upload_data import UploadDataJob

# Assuming running from same directory as this README file
cwd = os.getcwd()
behavior_path = Path(cwd) / "tests" / "resources" / "behavior_data"
ecephys_path = Path(cwd) / "tests" / "resources" / "ecephys_data"
metadata_path = Path(cwd) / "tests" / "resources" / "metadata_dir"

modality_directories = {
  "behavior": behavior_path,
  "ecephys": ecephys_path
}

metadata_directory = metadata_path

job_settings = JobSettings(
  dry_run=True,
  modality_directories=modality_directories,
  metadata_directory=metadata_directory,
  s3_bucket="aind-open-data-dev"
)

job = UploadDataJob(job_settings=job_settings)
job.run_job()

Example Command Line (Linux and MacOs)

python -m aind_data_transfer_lite.upload_data \
--metadata_directory "./tests/resources/metadata_dir" \
--modality_directories '{"behavior": "./tests/resources/behavior_data", "ecephys": "./tests/resources/ecephys_data"}' \
--dry_run "True"

Example Command Line (PowerShell)

python -m aind_data_transfer_lite.upload_data `
--metadata_directory "./tests/resources/metadata_dir" `
--modality_directories '{\"behavior\": \"./tests/resources/behavior_data\", \"ecephys\": \"./tests/resources/ecephys_data\"}' `
--dry_run "True"

Contributing

For code development, clone the repo and install as

pip install -e ".[dev]"

Linters and testing

There are several libraries used to run linters, check documentation, and run tests.

• Please test your changes using the coverage library, which will run the tests and log a coverage report:

coverage run -m unittest discover && coverage report

• Use interrogate to check that modules, methods, etc. have been documented thoroughly:

interrogate .

• Use flake8 to check that code is up to standards (no unused imports, etc.):

flake8 .

• Use black to automatically format the code into PEP standards:

black .

• Use isort to automatically sort import statements:

isort .

Pull requests

For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use Angular style for commit messages. Roughly, they should follow the pattern:

<type>(<scope>): <short summary>

where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:

• build: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
• ci: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
• docs: Documentation only changes
• feat: A new feature
• fix: A bugfix
• perf: A code change that improves performance
• refactor: A code change that neither fixes a bug nor adds a feature
• test: Adding missing tests or correcting existing tests

Semantic Release

The table below, from semantic release, shows which commit message gets you which release type when semantic-release runs (using the default configuration):

Commit message	Release type
fix(pencil): stop graphite breaking when too much pressure applied	Patch Fix Release, Default release
feat(pencil): add 'graphiteWidth' option	Minor Feature Release
perf(pencil): remove graphiteWidth option BREAKING CHANGE: The graphiteWidth option has been removed. The default graphite width of 10mm is always used for performance reasons.	Major Breaking Release (Note that the BREAKING CHANGE: token must be in the footer of the commit)