This is an implementation of the ga4gh-schemas using python generated gRPC bindings. The goal of this application is to present the bindings for implementing a GA4GH gateway. It does not provide an implementation to serve RPC requests or for adding genomics data to a datastore.

This will download a script to install protocol buffers with gRPC plugins.

curl -fsSL https://goo.gl/getgrpc | bash -s python

Then get a copy of the repository and create a virtual environment.

git clone https://github.com/david4096/ga4gh-grpc-python.git
cd ga4gh-grpc-python
virtualenv env
source env/bin/activate
pip install -r requirements.txt

The schemas are added as a submodule. For now, this means you can go to that directory and use git pull to get the latest from that repository. The protocol buffers bindings are currently checked in. To regenerate them you might run:

protoc -I schemas/src/main/proto --python_out=. --grpc_out=. --plugin=protoc-gen-grpc=`which grpc_python_plugin` schemas/src/main/proto/ga4gh/*

Start the read service with python read_service.py. Then, open another terminal and make sure to get back into the same virtual environment (source env/bin/activate).

Then you can run python client.py and you should see something like:

D0801 18:58:32.494901000 140735095906304 ev_posix.c:101] Using polling engine: poll
id: "echo"

E0801 18:58:32.562562000 140735095906304 chttp2_transport.c:1810] close_transport: {"created":"@1470103112.562539000","description":"FD shutdown","file":"src/core/lib/iomgr/ev_poll_posix.c","file_line":427}

Here, we've issued a request to the server and it has responded back with a read_group_set with the id from our request.

In the file read_service.py, there isn't much. To implement a method to service an RPC request, you can simply add it to the function here:

class ReadService(read_service_pb2.BetaReadServiceServicer):

  def SearchReadGroupSets(self, request, context):
    return read_service_pb2.SearchReadGroupSetsResponse()

  def GetReadGroupSet(self, request, context):
    return reads_pb2.ReadGroupSet(id=request.read_group_set_id)

For example, to change our response to include a name we could add:

    return reads_pb2.ReadGroupSet(id=request.read_group_set_id, name="my name")

We need to restart our server to reflect these changes (ctrl^c the tab with the server) and restart it using python read_service.py. Then rerunning python client.py we see something like:

D0801 19:07:06.385810000 140735095906304 ev_posix.c:101] Using polling engine: poll
id: "echo"
name: "my name"

E0801 19:07:06.454768000 140735095906304 chttp2_transport.c:1810] close_transport: {"created":"@1470103626.454738000","description":"FD shutdown","file":"src/core/lib/iomgr/ev_poll_posix.c","file_line":427}