umls-downloader 0.1.4

Automate downloading and extracting UMLS data

UMLS Downloader

Don't worry about UMLS Terminology Services (UTS) licensing and distribution rules - just use umls_downloader to write code that knows how to download content and use it automatically from the following (non-exhaustive) list of resources:

• UMLS
• RxNorm
• SemMedDB
• SNOMED-CT
• potentially more in the future

or any content that can be downloaded through the UTS ticket granting system. There's no centralized list of content available through the UTS so suggestions for additional resources are welcome through the issue tracker.

Full documentation are available at umls-downloader.readthedocs.io.

💪 Getting Started

Download A Specific Version of UMLS

import os
from umls_downloader import download_umls

# Get this from https://uts.nlm.nih.gov/uts/edit-profile
api_key = ...

path = download_umls(version="2021AB", api_key=api_key)

# This is where it gets downloaded: ~/.data/bio/umls/2021AB/umls-2021AB-mrconso.zip
expected_path = os.path.join(
    os.path.expanduser("~"), ".data", "umls", "2021AB",
    "umls-2021AB-mrconso.zip",
)
assert expected_path == path.as_posix()

After it's been downloaded once, it's smart and doesn't need to download again. It gets stored using pystow automatically in the ~/.data/bio/umls directory.

A full list of functions is available in the documentation.

Automating Configuration of UTS Credentials

There are two ways to automatically set the username and password so you don't have to worry about getting it and passing it around in your python code:

1. Set UMLS_API_KEY in the environment
2. Create ~/.config/umls.ini and set in the [umls] section a api_key key.

from umls_downloader import download_umls

# Same path as before
path = download_umls(version="2021AB")

Download the Latest Version

First, you'll have to install bioversions with pip install bioversions, whose job it is to look up the latest version of many databases. Then, you can modify the previous code slightly by omitting the version keyword argument:

from umls_downloader import download_umls

# Same path as before (as of November 21st, 2021)
path = download_umls()

Download and open the file

The UMLS file is zipped, so it's usually accompanied by the following boilerplate code:

import zipfile
from umls_downloader import download_umls

path = download_umls()
with zipfile.ZipFile(path) as zip_file:
    with zip_file.open("MRCONSO.RRF", mode="r") as file:
        for line in file:
            ...

This exact code is wrapped with the open_umls() using Python's context manager so it can more simply be written as:

from umls_downloader import open_umls

with open_umls() as file:
    for line in file:
        ...

The version and api_key arguments also apply here.

Command Line Interface

The umls-downloader command line tool is automatically installed. It can be used from the console with the --help flag to show all subcommands:

$ umls-downloader --help

TODO show the most useful thing the CLI does! The CLI will have documentation auto-generated by sphinx.

Why not an API?

The UMLS provides an API for access to tiny bits of data at a time. There are even two recent (last 5 years) packages umls-api connect-umls that provide a wrapper around them. However, API access is generally rate limited, difficult to use in bulk, and slow. For working with UMLS (or any other database, for that matter)in bulk, it's necessary to download full database dumps.

🚀 Installation

The most recent release can be installed from PyPI with uv:

$ uv pip install umls-downloader

or with pip:

$ python3 -m pip install umls-downloader

The most recent code and data can be installed directly from GitHub with uv:

$ uv pip install git+https://github.com/cthoyt/umls-downloader.git

or with pip:

$ python3 -m pip install git+https://github.com/cthoyt/umls-downloader.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

$ git clone git+https://github.com/cthoyt/umls-downloader.git
$ cd umls-downloader
$ uv pip install -e .

Alternatively, install using pip:

$ python3 -m pip install -e .

Pre-commit

You can optionally use pre-commit to automate running key code quality checks on each commit. Enable it with:

$ uvx pre-commit install

Or using pip:

$ pip install pre-commit
$ pre-commit install

🥼 Testing

After cloning the repository and installing tox with uv tool install tox --with tox-uv or python3 -m pip install tox tox-uv, the unit tests in the tests/ folder can be run reproducibly with:

$ tox -e py

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

$ git clone git+https://github.com/cthoyt/umls-downloader.git
$ cd umls-downloader
$ tox -e docs
$ open docs/build/html/index.html

The documentation automatically installs the package as well as the docs extra specified in the pyproject.toml. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

The documentation can be deployed to ReadTheDocs using this guide. The .readthedocs.yml YAML file contains all the configuration you'll need. You can also set up continuous integration on GitHub to check not only that Sphinx can build the documentation in an isolated environment (i.e., with tox -e docs-test) but also that ReadTheDocs can build it too.

🧑‍💻 For Maintainers

See maintainer instructions

Initial Configuration

Configuring ReadTheDocs

ReadTheDocs is an external documentation hosting service that integrates with GitHub's CI/CD. Do the following for each repository:

1. Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
4. Click next, and you're good to go!

Configuring Archival on Zenodo

Zenodo is a long-term archival system that assigns a DOI to each release of your package. Do the following for each repository:

1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant" next to any organizations you want to enable the integration for, then click the big green "approve" button. This step only needs to be done once.
2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make a new repository, you'll have to come back to this

After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate to https://zenodo.org/account/settings/github/repository/cthoyt/umls-downloader to see the DOI for the release and link to the Zenodo record for it.

Registering with the Python Package Index (PyPI)

The Python Package Index (PyPI) hosts packages so they can be easily installed with pip, uv, and equivalent tools.

1. Register for an account here
2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to the "re-send verification email" button
3. 2-Factor authentication is required for PyPI since the end of 2023 (see this blog post from PyPI). This means you have to first issue account recovery codes, then set up 2-factor authentication
4. Issue an API token from https://pypi.org/manage/account/token

This only needs to be done once per developer.

Configuring your machine's connection to PyPI

This needs to be done once per machine.

$ uv tool install keyring
$ keyring set https://upload.pypi.org/legacy/ __token__
$ keyring set https://test.pypi.org/legacy/ __token__

Note that this deprecates previous workflows using .pypirc.

📦 Making a Release

Uploading to PyPI

After installing the package in development mode and installing tox with uv tool install tox --with tox-uv or python3 -m pip install tox tox-uv, run the following from the console:

$ tox -e finish

This script does the following:

1. Uses bump-my-version to switch the version number in the pyproject.toml, src/umls_downloader/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using uv build
3. Uploads to PyPI using uv publish.
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion -- minor after.

Releasing on GitHub

1. Navigate to https://github.com/cthoyt/umls-downloader/releases/new to draft a new release
2. Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
3. Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit
4. Click the big green "Publish Release" button

This will trigger Zenodo to assign a DOI to your release as well.

Updating Package Boilerplate

This project uses cruft to keep boilerplate (i.e., configuration, contribution guidelines, documentation configuration) up-to-date with the upstream cookiecutter package. Install cruft with either uv tool install cruft or python3 -m pip install cruft then run:

$ cruft update

More info on Cruft's update command is available here.