Merge pull request #158 from Ensembl/server_reflection

added gRPC reflection to Thoas client

common/db.py

@@ -16,7 +16,8 @@
 import pymongo
 import mongomock
 import grpc
-from ensembl.production.metadata.grpc import ensembl_metadata_pb2_grpc
+
+from yagrc import reflector as yagrc_reflector
 
 from common.utils import process_release_version
 
@@ -117,8 +118,24 @@ def __init__(self, config):
             "{}:{}".format(host, port), options=(("grpc.enable_http_proxy", 0),)
         )
 
+        # create reflector for querying server using reflection
+        self.reflector = yagrc_reflector.GrpcReflectionClient()
+
+        # use reflection to load service definitions and message types
+        self.reflector.load_protocols(
+            self.channel, symbols=["ensembl_metadata.EnsemblMetadata"]
+        )
+
+        # dynamically retrieve the client stub class for service
+        stub_class = self.reflector.service_stub_class(
+            "ensembl_metadata.EnsemblMetadata"
+        )
+
         # bind the client and the server
-        self.stub = ensembl_metadata_pb2_grpc.EnsemblMetadataStub(self.channel)
+        self.stub = stub_class(self.channel)
 
     def get_grpc_stub(self):
         return self.stub
+
+    def get_grpc_reflector(self):
+        return self.reflector

common/extensions.py

@@ -33,6 +33,5 @@ def format(self, context):
             )
             return {
                 "execution_time_in_seconds": exec_time_in_secs,
-                "metadata_api_version": utils.get_ensembl_metadata_api_version(),
             }
         return None

common/utils.py

@@ -59,21 +59,6 @@ def process_release_version(grpc_response):
     return "release_" + release_version
 
 
-def get_ensembl_metadata_api_version():
-    """
-    Get the Metadata API tag from requirement.txt file
-    """
-    version = "unknown"  # default version
-    with open("requirements.txt", "r", encoding="UTF-8") as file:
-        lines = file.readlines()
-        for line in lines:
-            if "ensembl-metadata-api" in line:
-                # Extract the tag part from the line
-                version = line.strip().split("@")[-1]
-                break
-    return version
-
-
 def check_requested_fields(info: GraphQLResolveInfo, fields: List[str]) -> List[bool]:
     """
     Check if specific fields are requested in the GraphQL query.

graphql_service/resolver/gene_model.py

@@ -17,7 +17,6 @@
 from typing import Dict, Optional, List, Any, Mapping
 
 from ariadne import QueryType, ObjectType
-from ensembl.production.metadata.api.models import Genome
 from graphql import GraphQLResolveInfo, GraphQLError
 from pymongo.database import Database, Collection
 
@@ -868,7 +867,7 @@ def resolve_genome(_, info: GraphQLResolveInfo, by_genome_uuid: Dict[str, str])
 
 
 def create_genome_response(
-    genome: Genome,
+    genome,
     dataset_data: Optional[List] = None,
     assembly_data: Optional[Mapping[Any, Any]] = None,
 ) -> Dict:

graphql_service/server.py

@@ -64,7 +64,8 @@
 
 GRPC_SERVER = db.GRPCServiceClient(os.environ)
 GRPC_STUB = GRPC_SERVER.get_grpc_stub()
-GRPC_MODEL = grpc_model.GRPC_MODEL(GRPC_STUB)
+GRPC_REFLECTOR = GRPC_SERVER.get_grpc_reflector()
+GRPC_MODEL = grpc_model.GRPC_MODEL(GRPC_STUB, GRPC_REFLECTOR)
 
 EXECUTABLE_SCHEMA = prepare_executable_schema()
 

grpc_service/grpc_model.py

@@ -1,24 +1,28 @@
 import logging
 
-from ensembl.production.metadata.grpc import ensembl_metadata_pb2
-
 logger = logging.getLogger(__name__)
 
 
 class GRPC_MODEL:  # pylint: disable=invalid-name
-    def __init__(self, grpc_stub):
+    def __init__(self, grpc_stub, grpc_reflector):
         self.grpc_stub = grpc_stub
+        self.reflector = grpc_reflector
 
     def get_genome_by_genome_uuid(self, genome_uuid, release_version=None):
         logger.debug(
             "Received RPC for GetGenomeByUUID with genome_uuid: '%s', release: %s",
             genome_uuid,
             release_version,
         )
-        request = ensembl_metadata_pb2.GenomeUUIDRequest(
+        request_class = self.reflector.message_class(
+            "ensembl_metadata.GenomeUUIDRequest"
+        )
+
+        request = request_class(
             genome_uuid=genome_uuid, release_version=release_version
         )
         response = self.grpc_stub.GetGenomeByUUID(request)
+
         return response
 
     def get_genome_by_specific_keyword(
@@ -47,7 +51,12 @@ def get_genome_by_specific_keyword(
             species_taxonomy_id,
             release_version,
         )
-        request = ensembl_metadata_pb2.GenomeBySpecificKeywordRequest(
+
+        request_class = self.reflector.message_class(
+            "ensembl_metadata.GenomeBySpecificKeywordRequest"
+        )
+
+        request = request_class(
             tolid=tolid,
             assembly_accession_id=assembly_accession_id,
             assembly_name=assembly_name,
@@ -67,13 +76,19 @@ def get_datasets_list_by_uuid(self, genome_uuid, release_version=None):
             genome_uuid,
             release_version,
         )
-        request = ensembl_metadata_pb2.DatasetsRequest(
+        request_class = self.reflector.message_class("ensembl_metadata.DatasetsRequest")
+
+        request = request_class(
             genome_uuid=genome_uuid, release_version=release_version
         )
         response = self.grpc_stub.GetDatasetsListByUUID(request)
         return response
 
     def get_release_by_genome_uuid(self, genome_uuid):
-        request = ensembl_metadata_pb2.ReleaseVersionRequest(genome_uuid=genome_uuid)
+        request_class = self.reflector.message_class(
+            "ensembl_metadata.ReleaseVersionRequest"
+        )
+
+        request = request_class(genome_uuid=genome_uuid)
         response = self.grpc_stub.GetReleaseVersionByUUID(request)
         return response

mypy.ini

@@ -22,3 +22,5 @@ ignore_missing_imports = True
 [mypy-ensembl.production.metadata.*]
 ignore_missing_imports = True
 
+[mypy-yagrc.*]
+ignore_missing_imports = True

requirements.txt

@@ -5,8 +5,8 @@ aiodataloader==0.4.0
 ariadne==0.23
 python-dotenv==1.0.1
 uvicorn==0.18.1
-ensembl-metadata-api@git+https://github.com/Ensembl/[email protected]
 grpcio==1.66.1
 grpcio-tools==1.66.1
 ensembl-utils==0.4.4
 ensembl-py==2.1.3
+yagrc==1.1.2