ga4gh

library0.3.5pypypiunverified

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.

data serialization http-networking

pip install ga4gh==0.3.5

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · GA4GH

ga4gh

datapythonv0.3.5

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.

FlaskGA4GHApplication

✓ from ga4gh.server.frontend import FlaskGA4GHApplication

✗ from ga4gh.frontend import FlaskGA4GHApplication

Old import path removed in v0.3.5 due to modularization

configure

✓ from ga4gh.server.cli import configure

✗ from ga4gh.cli import configure

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

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()

ga4gh_server --version

Debug

Known issues

breakingPackage 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

affects: >=0.3.6

breakingIn 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.

affects: >=0.3.1

breakingIn 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.

affects: >=0.3.5

gotchaThe '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.

affects: >=0.3.5

Upgrade

Version history

0.3.5latest on PyPI · released Jan 24, 2017

Audit

Dependencies

grpciorequiredProtocol Buffers gRPC support

protobufrequiredProtocol Buffers serialization

flaskrequiredWeb server framework

Agent activity

18 hits · last 30 days

node

Resources

githubhttps://github.com/ga4gh/server ↗

packagehttps://pypi.org/project/ga4gh/ ↗

homepagehttps://ga4gh.org ↗