GA4GH Server

0.3.5 verified Sat May 09 auth: no python

A reference implementation of the Global Alliance for Genomics and Health (GA4GH) API for genomic data. Versions 0.3.x are alpha pre-releases with major breaking changes (protobuf migration, modularization, package rename). As of v0.3.6 the package is renamed to ga4gh-server on PyPI.

pip install ga4gh==0.3.5

Common errors

error ImportError: No module named 'ga4gh.frontend' ↓

cause Module structure changed in v0.3.5; frontend code moved under ga4gh.server.

fix

Use 'from ga4gh.server.frontend import FlaskGA4GHApplication'

error ModuleNotFoundError: No module named 'ga4gh' ↓

cause Package renaming to 'ga4gh-server' in v0.3.6; attempting to install 'ga4gh' no longer exists for newer versions.

fix

Run 'pip install ga4gh-server' instead of 'pip install ga4gh'

error AttributeError: module 'ga4gh' has no attribute 'schemas' ↓

cause Schemas extracted to separate package 'ga4gh-schemas' in v0.3.5.

fix

Install 'pip install ga4gh-schemas' and import from 'ga4gh.schemas'

Warnings

breaking Package renamed from 'ga4gh' to 'ga4gh-server' starting from v0.3.6. All future versions will be published as ga4gh-server. Install the new package for updates. ↓

fix pip uninstall ga4gh; pip install ga4gh-server

breaking In v0.3.1, the serialization format switched from Avro to Protocol Buffers. Existing data files and client applications are incompatible. ↓

fix Re-export data to Protobuf format; update clients to use protobuf instead of avro.

breaking In v0.3.5, the package was modularized into ga4gh, ga4gh-schemas, ga4gh-client, ga4gh-common. Import paths changed; old imports 'from ga4gh.frontend' no longer work. ↓

fix Change imports to 'from ga4gh.server.frontend' etc.

gotcha The 'ga4gh' package on PyPI is the server package, not a client library. For client functionality, use 'ga4gh-client' (pip install ga4gh-client). ↓

fix Install ga4gh-client for client API.

Install

pip install ga4gh-server

Imports

FlaskGA4GHApplication

wrong

from ga4gh.frontend import FlaskGA4GHApplication

correct

from ga4gh.server.frontend import FlaskGA4GHApplication

Old import path removed in v0.3.5 due to modularization

configure

wrong

from ga4gh.cli import configure

correct

from ga4gh.server.cli import configure

CLI moved to ga4gh.server.cli in v0.3.4

Quickstart

Initialize GA4GH server with Flask. Set GA4GH_CONFIG environment variable to point to your configuration file.

from ga4gh.server.frontend import FlaskGA4GHApplication
from ga4gh.server.cli import configure
import os

app = FlaskGA4GHApplication()
config = os.environ.get('GA4GH_CONFIG', 'config.py')
configure(app, config) 
app.run()