eutils

library0.6.1pypypi✓ verified 90d ago

Python interface to NCBI's E-utilities API (Entrez Programming Utilities). Current version 0.6.1, requires Python >=3.12. Supports searching, fetching, and linking NCBI databases (PubMed, Nucleotide, etc.). Release cadence is irregular.

database

pip install eutils

github ↗homepage ↗

INSTALL

IMPORT

SIG · EUTILS

eutils

databasepythonv0.6.1

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

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

Client

✓ from eutils import Client

Query

✓ from eutils import Query

Create a Client with email (required) and optional NCBI API key for higher rate limits, then search PubMed.

from eutils import Client # Use email to comply with NCBI's usage policy (required by eutils) client = Client(email='your_email@example.com', api_key=os.environ.get('NCBI_API_KEY', '')) result = client.esearch(db='pubmed', term='cancer', retmax=5) print(result)

Debug

Known issues

breakingeutils 0.6.x drops support for Python <3.12. Users on older Python versions must stay on 0.5.x or upgrade Python.

fix

Upgrade Python to 3.12+ or pin to eutils==0.5.4.

affects: >=0.6.0

gotchaNCBI requires an email address and, for high-volume access, an API key. eutils will warn if email is missing, and may block requests without proper identification.

fix

Always provide an email when creating a Client. For higher rate limits, register for an NCBI API key and pass it via `api_key` parameter.

affects: all

gotchaThe `efetch` method returns raw XML strings by default, not parsed objects. Users often expect Python objects and are surprised by the string output.

fix

Parse XML manually or use `eutils.xml_parser` helpers if available. Alternatively, use `eutils.xml_parser.parse_efetch_xml()` to get structured data.

affects: all

Errors

Common errors & fixes

EClientWarning: Email not provided. Please provide an email address.

Creating a Client without the `email` parameter. NCBI policy requires an email address.

fix

Initialize Client with email: `Client(email='your.email@example.com')`.

requests.exceptions.HTTPError: 429 Client Error: Too Many Requests

Exceeding NCBI's rate limit (3 requests/second without API key, 10 requests/second with API key).

fix

Add a delay between requests or obtain an NCBI API key and pass it to Client: `Client(api_key='your_key')`.

AttributeError: 'str' object has no attribute 'find' (when trying to parse efetch result)

Assuming `efetch` returns parsed data, but it returns raw XML string by default.

fix

Parse the XML string: `import xml.etree.ElementTree as ET; root = ET.fromstring(raw_xml)`.

Upgrade

Version history

0.6.1latest on PyPI · released Dec 7, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

14 hits · last 30 days

node

Resources

githubhttps://github.com/biocommons/eutils/ ↗

homepagehttps://github.com/biocommons/eutils/ ↗