v2.1.4

Download

• PyPI: https://pypi.org/project/omim-cli/2.1.4/
• pip install omim-cli==2.1.4

Changes

• Add 429 rate-limit retry (10s backoff, one retry) for both remote check and download
• Use HEAD + Last-Modified for fast-path change detection
• check_updates() returns (need, failed) so users can distinguish confirmed updates from check failures
• Print full download URL on HTTP errors for manual download
• Unify request rhythm: 1s sleep before every request

v2.1.3

What's Changed

Bug fixes

• Fixed omim-cli query returning empty output due to SQLAlchemy expire_on_commit=True clearing column values after session close
• Added isinstance(v, str) guard before json.loads(v) to prevent TypeError on NULL JSON fields

Upgrade

pip install -U omim-cli

OMIM-cli v2.1.2

What's Changed

Bug fixes

• Fixed omim-cli faq crash (NameError)
• Fixed omim-cli stats crash on empty database
• version.json missing/corrupt now raises an error instead of silently falling back to 0.0.0

Improvements

• omim-cli query: fixed file handle leak, removed duplicate DB queries, JSON output now preserves empty strings and
  0 values
• omim-cli update: fixed external_links marker so entries without external links are not permanently skipped;
  removed redundant commits during API enrichment
• Inheritance abbreviations now use short codes (PD, PR, SMu, SMo, Mu, IC, DD, DR)
• API responses that are not JSON (e.g. CAPTCHA pages) now show a clear error with a link to open in browser
• Database migration runs only once per session and validates identifiers against a whitelist

Docs

• Rewrote the outdated web-scraper section in docs/OMIM_API.md

omim-cli v2.1.1

omim-cli v2.1.1

Fixed

• Stop cleanly when the OMIM API quota is exhausted (429). Previously, a
  persistent 429 (daily quota used up) was caught as a generic error and the
  bulk update kept retrying every remaining batch — hammering the API and
  wasting a 10s backoff on each. Now a 429 that persists past the single retry
  raises a dedicated QuotaExhausted exception, and omim-cli update --with-api
  / --refresh abort the whole run gracefully:
  • already-fetched entries are committed (per-batch), so re-running later
    resumes from where it stopped (enriched entries are skipped)
  • a clear stopped early … re-run later to resume message is printed
• Non-429 errors still skip the batch, but 5 consecutive failures also abort
  to avoid endless looping on persistent errors.

Install

pip install -U omim-cli      # → 2.1.1

Full changelog: v2.1.0...v2.1.1

omim-cli v2.1.0

omim-cli v2.1.0

A client for OMIM (Online Mendelian Inheritance in Man) that obtains data
exclusively through official, legal channels — the OMIM REST API and the
official text-file downloads. No HTML scraping, no bundled/redistributed data.

Highlights

• Official data sources. mim2gene.txt / mimTitles.txt / genemap2.txt /
  morbidmap.txt provide structured data; the API provides text sections,
  clinical synopsis (with HPO/SNOMED/ICD ontology IDs), allelic variants,
  references, and 30+ external cross-references.
• Store everything. All source-provided fields are persisted (status,
  external_links, full gene record, dates, contributors, edit history, etc.).
• Incremental by design.
  • text import is skipped when files are unchanged
  • --with-api only enriches entries not yet enriched
  • --refresh probes dateUpdated in batches of 20 (include=dates) and
    re-fetches only entries OMIM has updated
• Commands: download, update, query, stats, faq, api
  (entry/search/gene-map/clinical-synopsis/allelic-variants/
  references/batch/config/status).
• Configurable DB path via OMIM_DB env var or --dbfile.

Install

pip install -U omim-cli          # Python ≥ 3.8
omim-cli api config --set-key YOUR_KEY   # free key from https://omim.org/downloads
omim-cli download
omim-cli update                  # add --with-api for deep content
omim-cli stats

Data & license

• Code: MIT (see LICENSE). Copyright © suqingdong (original omim) and Liozhang (omim-cli fork).
• OMIM data is copyrighted by Johns Hopkins University and is not
  redistributed by this package — each user downloads their own copy. Use of
  OMIM data is governed by the OMIM User Agreement.