Registry / data / umls-downloader

umls-downloader

library0.1.3pypypi✓ verified 88d ago

Automates downloading UMLS (Unified Medical Language System) data from the NLM, including MRCONSO.RRF, RxNorm, and SNOMED-CT. Current version 0.1.3, released Jan 2024. Monthly or ad-hoc releases.

data

pip install umls-downloader

github ↗package ↗

INSTALL

IMPORT

SIG · UMLS-DOWNLOADER

umls-downloader

datapythonv0.1.3

Install

2.9s avg

Import

1109ms

Disk

24MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.1.3 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 1.178s · 26.2MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 2.9s · import 1.040s · 27MB

24MB installed

● package 24MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

download_umls

✓ from umls_downloader import download_umls

✗ import umls_downloader ... umls_downloader.download_umls()

common but verbose; recommended import is from umls_downloader import download_umls

download_rxnorm

✓ from umls_downloader import download_rxnorm

✗ from umls_downloader.rxnorm import download_rxnorm

wrong: no submodule rxnorm; all functions are top-level

download_snomed

✓ from umls_downloader import download_snomed

✗ from umls_downloader import download_snomedct

wrong: function is download_snomed, not download_snomedct

Download UMLS Metathesaurus MRCONSO.RRF for a given release version. API key required.

from umls_downloader import download_umls # Requires UMLS API key from https://uts.nlm.nih.gov/uts/ # Set environment variable UMLS_API_KEY or pass directly path = download_umls(apikey='YOUR_API_KEY', version='2023AA') print(f'Downloaded MRCONSO.RRF to {path}')

Debug

Known issues

gotchaUMLS API key is required. Set environment variable UMLS_API_KEY or pass apikey argument. Without key, download fails with authentication error.

fix

Obtain API key from https://uts.nlm.nih.gov/uts/ and set as UMLS_API_KEY environment variable or pass as argument.

affects: all

breakingVersion 0.1.2 changed the MRCONSO.RRF download structure due to upstream UMLS changes. Older releases may fail with v2023AA+.

fix

Upgrade to >=0.1.2 for compatibility with current UMLS releases.

affects: <0.1.2

gotchadownload_umls returns the path to the downloaded RRF file (not a ZIP). The file is extracted from the UMLS ZIP automatically.

fix

Use returned path directly; no need to unzip manually.

affects: all

deprecatedVersion 0.0.2 introduced force_download parameter. In >=0.1.0, behavior changed: files are not re-downloaded by default. Use force=True to override.

fix

Pass force=True to download again if file exists.

affects: >=0.1.0

Errors

Common errors & fixes

UTSProfileError: Authentication error. Please check your UMLS API key.

Invalid or missing UMLS API key.

fix

Set UMLS_API_KEY environment variable or pass valid apikey to download function.

requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://download.nlm.nih.gov/umls/...

The requested UMLS version (e.g., '2020AA') is no longer available or the URL changed.

fix

Use a supported version (e.g., '2023AA' or latest). Check https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html

AttributeError: module 'umls_downloader' has no attribute 'download_snomedct'

The function is named download_snomed, not download_snomedct.

fix

Use download_snomed instead.

FileNotFoundError: [Errno 2] No such file or directory: 'MRCONSO.RRF' after download

The file is extracted inside a subdirectory (e.g., '2023AA/META/MRCONSO.RRF') but the function returns the wrong path in some versions.

fix

Update to latest version (0.1.3) and ensure you use the returned path directly.

Upgrade

Version history

0.1.3latest on PyPI · released Apr 2, 2024

Audit

Dependencies

requestsrequiredHTTP requests for UMLS TGT authentication and downloads

Agent activity

17 hits · last 30 days

node

Amazon

OpenAI (training)

Resources

githubhttps://github.com/cthoyt/umls_downloader ↗

packagehttps://pypi.org/project/umls-downloader/ ↗