diff --git a/cc/google/fhir/BUILD b/cc/google/fhir/BUILD index bc6a6c324..192a0df70 100644 --- a/cc/google/fhir/BUILD +++ b/cc/google/fhir/BUILD @@ -473,6 +473,7 @@ cc_test( "//proto/r4/core/resources:bundle_and_contained_resource_cc_proto", "//proto/stu3:datatypes_cc_proto", "//proto/stu3:extensions_cc_proto", + "//proto/stu3:ml_extensions_cc_proto", "//proto/stu3:resources_cc_proto", "//testdata/r4/profiles:test_cc_proto", "//testdata/stu3/profiles:test_cc_proto", diff --git a/cc/google/fhir/r4/BUILD b/cc/google/fhir/r4/BUILD index 8f434d8d8..45b172db5 100644 --- a/cc/google/fhir/r4/BUILD +++ b/cc/google/fhir/r4/BUILD @@ -106,7 +106,8 @@ cc_test( ":extensions", "//cc/google/fhir:test_helper", "//cc/google/fhir/testutil:proto_matchers", - "//proto/r4:google_extensions_cc_proto", + "//proto/r4:fhirproto_extensions_cc_proto", + "//proto/r4:ml_extensions_cc_proto", "//proto/r4/core:datatypes_cc_proto", "//proto/r4/core:extensions_cc_proto", "//proto/r4/core/resources:composition_cc_proto", @@ -136,7 +137,7 @@ cc_library( "//cc/google/fhir:util", "//cc/google/fhir/status", "//cc/google/fhir/status:statusor", - "//proto/r4:google_extensions_cc_proto", + "//proto/r4:fhirproto_extensions_cc_proto", "//proto/r4/core:datatypes_cc_proto", "//proto/r4/core/resources:bundle_and_contained_resource_cc_proto", "@com_google_absl//absl/memory", @@ -160,7 +161,7 @@ cc_test( "//cc/google/fhir:json_format", "//cc/google/fhir:test_helper", "//cc/google/fhir/testutil:proto_matchers", - "//proto/r4:google_extensions_cc_proto", + "//proto/r4:fhirproto_extensions_cc_proto", "//proto/r4/core:datatypes_cc_proto", "//proto/r4/core/resources:binary_cc_proto", "//proto/r4/core/resources:observation_cc_proto", diff --git a/cc/google/fhir/r4/extensions_test.cc b/cc/google/fhir/r4/extensions_test.cc index 120260f2a..9b5178646 100644 --- a/cc/google/fhir/r4/extensions_test.cc +++ b/cc/google/fhir/r4/extensions_test.cc @@ -25,7 +25,8 @@ #include "proto/r4/core/datatypes.pb.h" #include "proto/r4/core/extensions.pb.h" #include "proto/r4/core/resources/composition.pb.h" -#include "proto/r4/google_extensions.pb.h" +#include "proto/r4/fhirproto_extensions.pb.h" +#include "proto/r4/ml_extensions.pb.h" #include "testdata/r4/profiles/test_extensions.pb.h" namespace google { @@ -37,11 +38,11 @@ namespace { using core::CapabilityStatementSearchParameterCombination; using core::Composition; using core::Extension; -using google::Base64BinarySeparatorStride; -using google::EventLabel; -using google::EventTrigger; -using google::PrimitiveHasNoValue; +using fhirproto::Base64BinarySeparatorStride; +using fhirproto::PrimitiveHasNoValue; using ::google::fhir::testutil::EqualsProto; +using ml::EventLabel; +using ml::EventTrigger; using testing::DigitalMediaType; template diff --git a/cc/google/fhir/r4/primitive_handler.cc b/cc/google/fhir/r4/primitive_handler.cc index 33bd80936..b42d3b194 100644 --- a/cc/google/fhir/r4/primitive_handler.cc +++ b/cc/google/fhir/r4/primitive_handler.cc @@ -35,7 +35,7 @@ #include "google/fhir/status/statusor.h" #include "google/fhir/util.h" #include "proto/r4/core/datatypes.pb.h" -#include "proto/r4/google_extensions.pb.h" +#include "proto/r4/fhirproto_extensions.pb.h" #include "include/json/json.h" namespace google { @@ -50,7 +50,7 @@ StatusOr> R4PrimitiveHandler::GetWrapper( const Descriptor* target_descriptor) const { absl::optional> wrapper = primitives_internal::GetWrapperForR4Types< - core::Extension, core::Xhtml, google::Base64BinarySeparatorStride>( + core::Extension, core::Xhtml, fhirproto::Base64BinarySeparatorStride>( target_descriptor); if (wrapper.has_value()) { diff --git a/cc/google/fhir/r4/primitive_handler_test.cc b/cc/google/fhir/r4/primitive_handler_test.cc index e6332c628..c3cfcd90d 100644 --- a/cc/google/fhir/r4/primitive_handler_test.cc +++ b/cc/google/fhir/r4/primitive_handler_test.cc @@ -26,12 +26,12 @@ #include "google/fhir/json_format.h" #include "google/fhir/r4/json_format.h" #include "google/fhir/test_helper.h" +#include "google/fhir/testutil/proto_matchers.h" #include "proto/r4/core/datatypes.pb.h" #include "proto/r4/core/resources/binary.pb.h" #include "proto/r4/core/resources/observation.pb.h" #include "proto/r4/core/resources/patient.pb.h" -#include "proto/r4/google_extensions.pb.h" -#include "google/fhir/testutil/proto_matchers.h" +#include "proto/r4/fhirproto_extensions.pb.h" namespace google { namespace fhir { @@ -107,8 +107,8 @@ void TestJsonValidation() { template void AddPrimitiveHasNoValue(W* primitive) { Extension* e = primitive->add_extension(); - e->mutable_url()->set_value( - GetStructureDefinitionUrl(r4::google::PrimitiveHasNoValue::descriptor())); + e->mutable_url()->set_value(GetStructureDefinitionUrl( + r4::fhirproto::PrimitiveHasNoValue::descriptor())); e->mutable_value()->mutable_boolean()->set_value(true); } diff --git a/cc/google/fhir/seqex/BUILD b/cc/google/fhir/seqex/BUILD index 1eb11cd16..2c98be89c 100644 --- a/cc/google/fhir/seqex/BUILD +++ b/cc/google/fhir/seqex/BUILD @@ -207,7 +207,8 @@ cc_library( ":resource_to_example", ":text_tokenizer", "//cc/google/fhir/stu3:primitive_handler", - "//proto/stu3:extensions_cc_proto", + "//proto/stu3:fhirproto_extensions_cc_proto", + "//proto/stu3:ml_extensions_cc_proto", "//proto/stu3:resources_cc_proto", "@com_google_absl//absl/status", ], @@ -224,7 +225,7 @@ cc_library( ":resource_to_example", ":text_tokenizer", "//cc/google/fhir/r4:primitive_handler", - "//proto/r4:google_extensions_cc_proto", + "//proto/r4:ml_extensions_cc_proto", "//proto/r4/core/resources:bundle_and_contained_resource_cc_proto", "//proto/r4/core/resources:claim_cc_proto", "//proto/r4/core/resources:composition_cc_proto", diff --git a/cc/google/fhir/seqex/r4.h b/cc/google/fhir/seqex/r4.h index b60bdb53b..56b9276e4 100644 --- a/cc/google/fhir/seqex/r4.h +++ b/cc/google/fhir/seqex/r4.h @@ -35,7 +35,7 @@ #include "proto/r4/core/resources/patient.pb.h" #include "proto/r4/core/resources/procedure.pb.h" #include "proto/r4/core/resources/service_request.pb.h" -#include "proto/r4/google_extensions.pb.h" +#include "proto/r4/ml_extensions.pb.h" namespace google { namespace fhir { @@ -51,8 +51,8 @@ inline void ResourceToExample(const google::protobuf::Message& message, ::google::fhir::r4::R4PrimitiveHandler::GetInstance()); } -typedef seqex::ConverterTypes ConverterTypes; diff --git a/cc/google/fhir/seqex/stu3.h b/cc/google/fhir/seqex/stu3.h index be0a96be4..17b36b8bf 100644 --- a/cc/google/fhir/seqex/stu3.h +++ b/cc/google/fhir/seqex/stu3.h @@ -24,7 +24,8 @@ #include "google/fhir/seqex/resource_to_example.h" #include "google/fhir/seqex/text_tokenizer.h" #include "google/fhir/stu3/primitive_handler.h" -#include "proto/stu3/google_extensions.pb.h" +#include "proto/stu3/fhirproto_extensions.pb.h" +#include "proto/stu3/ml_extensions.pb.h" #include "proto/stu3/resources.pb.h" namespace google { @@ -41,8 +42,8 @@ inline void ResourceToExample(const google::protobuf::Message& message, ::google::fhir::stu3::Stu3PrimitiveHandler::GetInstance()); } -typedef seqex::ConverterTypes ConverterTypes; diff --git a/cc/google/fhir/stu3/BUILD b/cc/google/fhir/stu3/BUILD index 5abf1d1f2..45755710a 100644 --- a/cc/google/fhir/stu3/BUILD +++ b/cc/google/fhir/stu3/BUILD @@ -103,6 +103,8 @@ cc_test( "//cc/google/fhir/testutil:proto_matchers", "//proto/stu3:datatypes_cc_proto", "//proto/stu3:extensions_cc_proto", + "//proto/stu3:fhirproto_extensions_cc_proto", + "//proto/stu3:ml_extensions_cc_proto", "//proto/stu3:resources_cc_proto", "//testdata/stu3/profiles:test_cc_proto", "@com_google_absl//absl/status", @@ -129,7 +131,7 @@ cc_library( "//cc/google/fhir/status", "//cc/google/fhir/status:statusor", "//proto/stu3:datatypes_cc_proto", - "//proto/stu3:extensions_cc_proto", + "//proto/stu3:fhirproto_extensions_cc_proto", "//proto/stu3:resources_cc_proto", "@com_google_absl//absl/memory", "@com_google_absl//absl/status", @@ -222,7 +224,7 @@ cc_test( "//cc/google/fhir/testutil:proto_matchers", "//proto/stu3:codes_cc_proto", "//proto/stu3:datatypes_cc_proto", - "//proto/stu3:extensions_cc_proto", + "//proto/stu3:fhirproto_extensions_cc_proto", "//proto/stu3:resources_cc_proto", "@com_google_absl//absl/strings", "@com_google_googletest//:gtest_main", diff --git a/cc/google/fhir/stu3/extensions_test.cc b/cc/google/fhir/stu3/extensions_test.cc index eb2b85aa1..e3cbcd4d8 100644 --- a/cc/google/fhir/stu3/extensions_test.cc +++ b/cc/google/fhir/stu3/extensions_test.cc @@ -24,7 +24,8 @@ #include "google/fhir/testutil/proto_matchers.h" #include "proto/stu3/datatypes.pb.h" #include "proto/stu3/extensions.pb.h" -#include "proto/stu3/google_extensions.pb.h" +#include "proto/stu3/fhirproto_extensions.pb.h" +#include "proto/stu3/ml_extensions.pb.h" #include "proto/stu3/resources.pb.h" #include "testdata/stu3/profiles/test_extensions.pb.h" @@ -34,11 +35,11 @@ namespace stu3 { namespace { -using google::Base64BinarySeparatorStride; -using google::EventLabel; -using google::EventTrigger; -using google::PrimitiveHasNoValue; +using fhirproto::Base64BinarySeparatorStride; +using fhirproto::PrimitiveHasNoValue; using ::google::fhir::testutil::EqualsProto; +using ml::EventLabel; +using ml::EventTrigger; using proto::CapabilityStatementSearchParameterCombination; using proto::Composition; using testing::DigitalMediaType; diff --git a/cc/google/fhir/stu3/primitive_handler.cc b/cc/google/fhir/stu3/primitive_handler.cc index b73564a2e..7019e68e9 100644 --- a/cc/google/fhir/stu3/primitive_handler.cc +++ b/cc/google/fhir/stu3/primitive_handler.cc @@ -35,7 +35,7 @@ #include "google/fhir/status/statusor.h" #include "google/fhir/util.h" #include "proto/stu3/datatypes.pb.h" -#include "proto/stu3/google_extensions.pb.h" +#include "proto/stu3/fhirproto_extensions.pb.h" #include "include/json/json.h" namespace google { @@ -50,8 +50,8 @@ StatusOr> Stu3PrimitiveHandler::GetWrapper( const Descriptor* target_descriptor) const { absl::optional> wrapper = primitives_internal::GetWrapperForStu3Types< - proto::Extension, proto::Xhtml, google::Base64BinarySeparatorStride>( - target_descriptor); + proto::Extension, proto::Xhtml, + fhirproto::Base64BinarySeparatorStride>(target_descriptor); if (wrapper.has_value()) { return std::move(wrapper.value()); diff --git a/cc/google/fhir/stu3/primitive_handler_test.cc b/cc/google/fhir/stu3/primitive_handler_test.cc index ad91babb3..d34b187e6 100644 --- a/cc/google/fhir/stu3/primitive_handler_test.cc +++ b/cc/google/fhir/stu3/primitive_handler_test.cc @@ -29,11 +29,11 @@ #include "google/fhir/json_format.h" #include "google/fhir/stu3/json_format.h" #include "google/fhir/test_helper.h" +#include "google/fhir/testutil/proto_matchers.h" #include "proto/stu3/codes.pb.h" #include "proto/stu3/datatypes.pb.h" -#include "proto/stu3/google_extensions.pb.h" +#include "proto/stu3/fhirproto_extensions.pb.h" #include "proto/stu3/resources.pb.h" -#include "google/fhir/testutil/proto_matchers.h" namespace google { namespace fhir { @@ -110,7 +110,7 @@ template void AddPrimitiveHasNoValue(W* primitive) { Extension* e = primitive->add_extension(); e->mutable_url()->set_value(GetStructureDefinitionUrl( - stu3::google::PrimitiveHasNoValue::descriptor())); + stu3::fhirproto::PrimitiveHasNoValue::descriptor())); e->mutable_value()->mutable_boolean()->set_value(true); } diff --git a/examples/gcp_datalab/02-gen-fhirdependencies.sh b/examples/gcp_datalab/02-gen-fhirdependencies.sh index fbd84e5de..f7c51579e 100755 --- a/examples/gcp_datalab/02-gen-fhirdependencies.sh +++ b/examples/gcp_datalab/02-gen-fhirdependencies.sh @@ -46,7 +46,7 @@ mkdir out-bin cp -fr bazel-bin/py ./out-bin/. cp -fr bazel-bin/proto ./out-bin/. -#Importing google_extensions_pb2 +#Importing fhirproto_extensions_pb2 touch ./out-genfiles/proto/__init__.py touch ./out-genfiles/proto/stu3/__init__.py diff --git a/examples/gcp_datalab/notebooks/1_train_and_eval_ml_model_to_predict_los.ipynb b/examples/gcp_datalab/notebooks/1_train_and_eval_ml_model_to_predict_los.ipynb index 1ede262c4..0691eee2e 100644 --- a/examples/gcp_datalab/notebooks/1_train_and_eval_ml_model_to_predict_los.ipynb +++ b/examples/gcp_datalab/notebooks/1_train_and_eval_ml_model_to_predict_los.ipynb @@ -90,7 +90,7 @@ "import time\n", "\n", "from proto import version_config_pb2\n", - "from proto.stu3 import google_extensions_pb2\n", + "from proto.stu3 import fhirproto_extensions_pb2\n", "from proto.stu3 import resources_pb2\n", "\n", "from google.protobuf import text_format\n", @@ -251,7 +251,7 @@ "\n", "_ = labels | beam.io.WriteToTFRecord(\n", " LABELS_PATH,\n", - " coder=beam.coders.ProtoCoder(google_extensions_pb2.EventLabel),\n", + " coder=beam.coders.ProtoCoder(fhirproto_extensions_pb2.EventLabel),\n", " file_name_suffix='.tfrecords')" ] }, @@ -486,7 +486,7 @@ "event_labels = ( \n", " p1 | 'readEventLabels' >> beam.io.ReadFromTFRecord(\n", " TF_RECORD_LABELS,\n", - " coder=beam.coders.ProtoCoder(google_extensions_pb2.EventLabel)))\n", + " coder=beam.coders.ProtoCoder(fhirproto_extensions_pb2.EventLabel)))\n", "\n", "keyed_event_labels = bundle_to_seqex.CreateTriggerLabelsPairLists(\n", " event_labels)\n", diff --git a/examples/gcp_datalab/notebooks/2_deploy_and_run_ml_model_to_predict_los.ipynb b/examples/gcp_datalab/notebooks/2_deploy_and_run_ml_model_to_predict_los.ipynb index 700ed7b46..8c084b6b1 100644 --- a/examples/gcp_datalab/notebooks/2_deploy_and_run_ml_model_to_predict_los.ipynb +++ b/examples/gcp_datalab/notebooks/2_deploy_and_run_ml_model_to_predict_los.ipynb @@ -93,7 +93,7 @@ "import time\n", "\n", "from proto import version_config_pb2\n", - "from proto.stu3 import google_extensions_pb2\n", + "from proto.stu3 import fhirproto_extensions_pb2\n", "from proto.stu3 import resources_pb2\n", "\n", "from google.protobuf import text_format\n", diff --git a/go/google/fhir/jsonformat/BUILD b/go/jsonformat/BUILD similarity index 85% rename from go/google/fhir/jsonformat/BUILD rename to go/jsonformat/BUILD index 4e05de985..fd6c2dce9 100644 --- a/go/google/fhir/jsonformat/BUILD +++ b/go/jsonformat/BUILD @@ -16,16 +16,16 @@ go_library( "unmarshaller.go", "version_config.go", ], - importpath = "google/fhir/jsonformat/jsonformat", + importpath = "github.com/google/fhir/go/jsonformat", deps = [ - "//go/google/fhir/jsonformat/internal/accessor", - "//go/google/fhir/jsonformat/internal/jsonpbhelper", + "//go/jsonformat/internal/accessor", + "//go/jsonformat/internal/jsonpbhelper", "//proto:annotations_go_proto", - "//proto/r4:google_extensions_go_proto", + "//proto/r4:fhirproto_extensions_go_proto", "//proto/r4/core:datatypes_go_proto", "//proto/r4/core/resources:bundle_and_contained_resource_go_proto", "//proto/stu3:datatypes_go_proto", - "//proto/stu3:extensions_go_proto", + "//proto/stu3:fhirproto_extensions_go_proto", "//proto/stu3:resources_go_proto", "@com_bitbucket_creachadair_stringset//:go_default_library", "@com_github_golang_protobuf//proto:go_default_library", @@ -48,13 +48,13 @@ go_test( ], embed = [":jsonformat"], deps = [ - "//go/google/fhir/jsonformat/internal/accessor", - "//go/google/fhir/jsonformat/internal/jsonpbhelper", + "//go/jsonformat/internal/accessor", + "//go/jsonformat/internal/jsonpbhelper", "//proto:annotations_go_proto", - "//proto/r4:google_extensions_go_proto", + "//proto/r4:fhirproto_extensions_go_proto", "//proto/r4/core:datatypes_go_proto", "//proto/stu3:datatypes_go_proto", - "//proto/stu3:extensions_go_proto", + "//proto/stu3:fhirproto_extensions_go_proto", "@com_github_golang_protobuf//proto:go_default_library", "@com_github_google_go_cmp//cmp:go_default_library", "@org_golang_google_protobuf//reflect/protoreflect:go_default_library", @@ -71,7 +71,7 @@ go_test( ], embed = [":jsonformat"], deps = [ - "//go/google/fhir/jsonformat/internal/jsonpbhelper", + "//go/jsonformat/internal/jsonpbhelper", "//proto/dstu2:codes_go_proto", "//proto/dstu2:datatypes_go_proto", "//proto/dstu2:metadatatypes_go_proto", diff --git a/go/google/fhir/jsonformat/date_time.go b/go/jsonformat/date_time.go similarity index 99% rename from go/google/fhir/jsonformat/date_time.go rename to go/jsonformat/date_time.go index 4d591b9cd..d9efaecbc 100644 --- a/go/google/fhir/jsonformat/date_time.go +++ b/go/jsonformat/date_time.go @@ -20,8 +20,8 @@ import ( "fmt" "time" - "google/fhir/jsonformat/internal/accessor/accessor" - "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper" + "github.com/google/fhir/go/jsonformat/internal/accessor" + "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper" "github.com/golang/protobuf/proto" "google.golang.org/protobuf/reflect/protoreflect" ) diff --git a/go/google/fhir/jsonformat/date_time_test.go b/go/jsonformat/date_time_test.go similarity index 99% rename from go/google/fhir/jsonformat/date_time_test.go rename to go/jsonformat/date_time_test.go index 800495ff6..510964469 100644 --- a/go/google/fhir/jsonformat/date_time_test.go +++ b/go/jsonformat/date_time_test.go @@ -20,7 +20,7 @@ import ( "testing" "time" - "google/fhir/jsonformat/internal/accessor/accessor" + "github.com/google/fhir/go/jsonformat/internal/accessor" "github.com/golang/protobuf/proto" "google.golang.org/protobuf/reflect/protoreflect" diff --git a/go/google/fhir/jsonformat/internal/accessor/BUILD b/go/jsonformat/internal/accessor/BUILD similarity index 88% rename from go/google/fhir/jsonformat/internal/accessor/BUILD rename to go/jsonformat/internal/accessor/BUILD index 19937111d..686a3d4b1 100644 --- a/go/google/fhir/jsonformat/internal/accessor/BUILD +++ b/go/jsonformat/internal/accessor/BUILD @@ -8,7 +8,7 @@ load("@io_bazel_rules_go//proto:def.bzl", "go_proto_library") go_library( name = "accessor", srcs = ["getter_setter.go"], - importpath = "google/fhir/jsonformat/internal/accessor/accessor", + importpath = "github.com/google/fhir/go/jsonformat/internal/accessor", deps = [ "@com_github_golang_protobuf//proto:go_default_library", "@com_github_pkg_errors//:go_default_library", @@ -38,6 +38,6 @@ proto_library( go_proto_library( name = "accessor_test_go_proto", - importpath = "google/fhir/jsonformat/internal/accessor/accessor_test_go_proto", + importpath = "jsonformat/internal/accessor/accessor_test_go_proto", proto = ":accessor_test_proto", ) diff --git a/go/google/fhir/jsonformat/internal/accessor/accessor_test.proto b/go/jsonformat/internal/accessor/accessor_test.proto similarity index 100% rename from go/google/fhir/jsonformat/internal/accessor/accessor_test.proto rename to go/jsonformat/internal/accessor/accessor_test.proto diff --git a/go/google/fhir/jsonformat/internal/accessor/getter_setter.go b/go/jsonformat/internal/accessor/getter_setter.go similarity index 100% rename from go/google/fhir/jsonformat/internal/accessor/getter_setter.go rename to go/jsonformat/internal/accessor/getter_setter.go diff --git a/go/google/fhir/jsonformat/internal/accessor/getter_setter_test.go b/go/jsonformat/internal/accessor/getter_setter_test.go similarity index 99% rename from go/google/fhir/jsonformat/internal/accessor/getter_setter_test.go rename to go/jsonformat/internal/accessor/getter_setter_test.go index 32a6e6720..96ed4c68a 100644 --- a/go/google/fhir/jsonformat/internal/accessor/getter_setter_test.go +++ b/go/jsonformat/internal/accessor/getter_setter_test.go @@ -24,7 +24,7 @@ import ( "github.com/golang/protobuf/proto" "google.golang.org/protobuf/testing/protocmp" - atpb "google/fhir/jsonformat/internal/accessor/accessor_test_go_proto" + atpb "jsonformat/internal/accessor/accessor_test_go_proto" d3pb "google/fhir/proto/stu3/datatypes_go_proto" r3pb "google/fhir/proto/stu3/resources_go_proto" ) diff --git a/go/google/fhir/jsonformat/internal/jsonpbhelper/BUILD b/go/jsonformat/internal/jsonpbhelper/BUILD similarity index 93% rename from go/google/fhir/jsonformat/internal/jsonpbhelper/BUILD rename to go/jsonformat/internal/jsonpbhelper/BUILD index dd3621c1a..862a05d4c 100644 --- a/go/google/fhir/jsonformat/internal/jsonpbhelper/BUILD +++ b/go/jsonformat/internal/jsonpbhelper/BUILD @@ -10,7 +10,7 @@ go_library( "fhirutil.go", "json_format.go", ], - importpath = "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper", + importpath = "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper", deps = [ "//proto:annotations_go_proto", "//proto/r4/core:datatypes_go_proto", @@ -42,7 +42,7 @@ go_test( "//proto/r4/core/resources:patient_go_proto", "//proto/stu3:codes_go_proto", "//proto/stu3:datatypes_go_proto", - "//proto/stu3:extensions_go_proto", + "//proto/stu3:fhirproto_extensions_go_proto", "//proto/stu3:resources_go_proto", "@com_github_golang_protobuf//proto:go_default_library", "@com_github_google_go_cmp//cmp:go_default_library", diff --git a/go/google/fhir/jsonformat/internal/jsonpbhelper/fhirutil.go b/go/jsonformat/internal/jsonpbhelper/fhirutil.go similarity index 100% rename from go/google/fhir/jsonformat/internal/jsonpbhelper/fhirutil.go rename to go/jsonformat/internal/jsonpbhelper/fhirutil.go diff --git a/go/google/fhir/jsonformat/internal/jsonpbhelper/fhirutil_test.go b/go/jsonformat/internal/jsonpbhelper/fhirutil_test.go similarity index 99% rename from go/google/fhir/jsonformat/internal/jsonpbhelper/fhirutil_test.go rename to go/jsonformat/internal/jsonpbhelper/fhirutil_test.go index 290536bc8..91f6d4fe9 100644 --- a/go/google/fhir/jsonformat/internal/jsonpbhelper/fhirutil_test.go +++ b/go/jsonformat/internal/jsonpbhelper/fhirutil_test.go @@ -30,7 +30,7 @@ import ( r4patientpb "google/fhir/proto/r4/core/resources/patient_go_proto" c3pb "google/fhir/proto/stu3/codes_go_proto" d3pb "google/fhir/proto/stu3/datatypes_go_proto" - e3pb "google/fhir/proto/stu3/extensions_go_proto" + e3pb "google/fhir/proto/stu3/fhirproto_extensions_go_proto" r3pb "google/fhir/proto/stu3/resources_go_proto" ) diff --git a/go/google/fhir/jsonformat/internal/jsonpbhelper/json_format.go b/go/jsonformat/internal/jsonpbhelper/json_format.go similarity index 100% rename from go/google/fhir/jsonformat/internal/jsonpbhelper/json_format.go rename to go/jsonformat/internal/jsonpbhelper/json_format.go diff --git a/go/google/fhir/jsonformat/internal/jsonpbhelper/json_format_test.go b/go/jsonformat/internal/jsonpbhelper/json_format_test.go similarity index 100% rename from go/google/fhir/jsonformat/internal/jsonpbhelper/json_format_test.go rename to go/jsonformat/internal/jsonpbhelper/json_format_test.go diff --git a/go/google/fhir/jsonformat/internal/protopath/BUILD b/go/jsonformat/internal/protopath/BUILD similarity index 89% rename from go/google/fhir/jsonformat/internal/protopath/BUILD rename to go/jsonformat/internal/protopath/BUILD index ed79f1ab5..68d48e409 100644 --- a/go/google/fhir/jsonformat/internal/protopath/BUILD +++ b/go/jsonformat/internal/protopath/BUILD @@ -14,14 +14,14 @@ proto_library( go_proto_library( name = "protopathtest_go_proto", - importpath = "google/fhir/jsonformat/internal/protopath/protopathtest_go_proto", + importpath = "jsonformat/internal/protopath/protopathtest_go_proto", proto = ":protopathtest_proto", ) go_library( name = "protopath", srcs = ["proto_path.go"], - importpath = "google/fhir/jsonformat/internal/protopath/protopath", + importpath = "github.com/google/fhir/go/jsonformat/internal/protopath", deps = [ "@com_github_golang_protobuf//proto:go_default_library", "@com_github_serenize_snaker//:go_default_library", diff --git a/go/google/fhir/jsonformat/internal/protopath/proto_path.go b/go/jsonformat/internal/protopath/proto_path.go similarity index 100% rename from go/google/fhir/jsonformat/internal/protopath/proto_path.go rename to go/jsonformat/internal/protopath/proto_path.go diff --git a/go/google/fhir/jsonformat/internal/protopath/proto_path_test.go b/go/jsonformat/internal/protopath/proto_path_test.go similarity index 99% rename from go/google/fhir/jsonformat/internal/protopath/proto_path_test.go rename to go/jsonformat/internal/protopath/proto_path_test.go index 9db803ce0..9fbe30cb2 100644 --- a/go/google/fhir/jsonformat/internal/protopath/proto_path_test.go +++ b/go/jsonformat/internal/protopath/proto_path_test.go @@ -23,7 +23,7 @@ import ( "google.golang.org/protobuf/proto" "google.golang.org/protobuf/testing/protocmp" - pptpb "google/fhir/jsonformat/internal/protopath/protopathtest_go_proto" + pptpb "jsonformat/internal/protopath/protopathtest_go_proto" rdpb "google/fhir/proto/stu3/datatypes_go_proto" rfpb "google/fhir/proto/stu3/resources_go_proto" ) diff --git a/go/google/fhir/jsonformat/internal/protopath/proto_path_test.proto b/go/jsonformat/internal/protopath/proto_path_test.proto similarity index 100% rename from go/google/fhir/jsonformat/internal/protopath/proto_path_test.proto rename to go/jsonformat/internal/protopath/proto_path_test.proto diff --git a/go/google/fhir/jsonformat/marshaller.go b/go/jsonformat/marshaller.go similarity index 99% rename from go/google/fhir/jsonformat/marshaller.go rename to go/jsonformat/marshaller.go index c13c8b9a7..817f44ca9 100644 --- a/go/google/fhir/jsonformat/marshaller.go +++ b/go/jsonformat/marshaller.go @@ -19,8 +19,8 @@ import ( "fmt" "strings" - "google/fhir/jsonformat/internal/accessor/accessor" - "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper" + "github.com/google/fhir/go/jsonformat/internal/accessor" + "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper" "github.com/golang/protobuf/proto" "github.com/golang/protobuf/ptypes" "google.golang.org/protobuf/reflect/protoreflect" diff --git a/go/google/fhir/jsonformat/marshaller_test.go b/go/jsonformat/marshaller_test.go similarity index 99% rename from go/google/fhir/jsonformat/marshaller_test.go rename to go/jsonformat/marshaller_test.go index 8127409f9..1a38e6b74 100644 --- a/go/google/fhir/jsonformat/marshaller_test.go +++ b/go/jsonformat/marshaller_test.go @@ -18,7 +18,7 @@ import ( "bytes" "testing" - "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper" + "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper" "github.com/google/go-cmp/cmp" "github.com/golang/protobuf/proto" "github.com/golang/protobuf/ptypes" diff --git a/go/google/fhir/jsonformat/primitive.go b/go/jsonformat/primitive.go similarity index 98% rename from go/google/fhir/jsonformat/primitive.go rename to go/jsonformat/primitive.go index 3a220ae15..edc634f36 100644 --- a/go/google/fhir/jsonformat/primitive.go +++ b/go/jsonformat/primitive.go @@ -21,8 +21,8 @@ import ( "sort" "strings" - "google/fhir/jsonformat/internal/accessor/accessor" - "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper" + "github.com/google/fhir/go/jsonformat/internal/accessor" + "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper" "github.com/golang/protobuf/proto" "google.golang.org/protobuf/reflect/protoreflect" ) diff --git a/go/google/fhir/jsonformat/primitive_test.go b/go/jsonformat/primitive_test.go similarity index 98% rename from go/google/fhir/jsonformat/primitive_test.go rename to go/jsonformat/primitive_test.go index 482909029..64a13476c 100644 --- a/go/google/fhir/jsonformat/primitive_test.go +++ b/go/jsonformat/primitive_test.go @@ -19,17 +19,17 @@ import ( "strconv" "testing" - "google/fhir/jsonformat/internal/accessor/accessor" - "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper" + "github.com/google/fhir/go/jsonformat/internal/accessor" + "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper" "github.com/google/go-cmp/cmp" "github.com/golang/protobuf/proto" "google.golang.org/protobuf/reflect/protoreflect" "google.golang.org/protobuf/testing/protocmp" d4pb "google/fhir/proto/r4/core/datatypes_go_proto" - e4pb "google/fhir/proto/r4/google_extensions_go_proto" + e4pb "google/fhir/proto/r4/fhirproto_extensions_go_proto" d3pb "google/fhir/proto/stu3/datatypes_go_proto" - e3pb "google/fhir/proto/stu3/extensions_go_proto" + e3pb "google/fhir/proto/stu3/fhirproto_extensions_go_proto" ) func appendSeparatorAndStrideExtensions(extListOwner protoreflect.Message, sep string, stride uint32) { diff --git a/go/google/fhir/jsonformat/r3_utils.go b/go/jsonformat/r3_utils.go similarity index 96% rename from go/google/fhir/jsonformat/r3_utils.go rename to go/jsonformat/r3_utils.go index e81108605..e245eba7e 100644 --- a/go/google/fhir/jsonformat/r3_utils.go +++ b/go/jsonformat/r3_utils.go @@ -21,7 +21,7 @@ import ( "bitbucket.org/creachadair/stringset" dpb "google/fhir/proto/stu3/datatypes_go_proto" - epb "google/fhir/proto/stu3/extensions_go_proto" + epb "google/fhir/proto/stu3/fhirproto_extensions_go_proto" rpb "google/fhir/proto/stu3/resources_go_proto" ) diff --git a/go/google/fhir/jsonformat/r4_utils.go b/go/jsonformat/r4_utils.go similarity index 98% rename from go/google/fhir/jsonformat/r4_utils.go rename to go/jsonformat/r4_utils.go index 1e44a28ca..222eea68b 100644 --- a/go/google/fhir/jsonformat/r4_utils.go +++ b/go/jsonformat/r4_utils.go @@ -24,7 +24,7 @@ import ( dpb "google/fhir/proto/r4/core/datatypes_go_proto" rpb "google/fhir/proto/r4/core/resources/bundle_and_contained_resource_go_proto" - epb "google/fhir/proto/r4/google_extensions_go_proto" + epb "google/fhir/proto/r4/fhirproto_extensions_go_proto" ) const ( diff --git a/go/google/fhir/jsonformat/reference.go b/go/jsonformat/reference.go similarity index 98% rename from go/google/fhir/jsonformat/reference.go rename to go/jsonformat/reference.go index af082aceb..f41a47423 100644 --- a/go/google/fhir/jsonformat/reference.go +++ b/go/jsonformat/reference.go @@ -18,8 +18,8 @@ import ( "fmt" "strings" - "google/fhir/jsonformat/internal/accessor/accessor" - "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper" + "github.com/google/fhir/go/jsonformat/internal/accessor" + "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper" "github.com/golang/protobuf/proto" "google.golang.org/protobuf/reflect/protoreflect" diff --git a/go/google/fhir/jsonformat/reference_test.go b/go/jsonformat/reference_test.go similarity index 100% rename from go/google/fhir/jsonformat/reference_test.go rename to go/jsonformat/reference_test.go diff --git a/go/google/fhir/jsonformat/test/BUILD b/go/jsonformat/test/BUILD similarity index 87% rename from go/google/fhir/jsonformat/test/BUILD rename to go/jsonformat/test/BUILD index b6d88a179..f74237ce2 100644 --- a/go/google/fhir/jsonformat/test/BUILD +++ b/go/jsonformat/test/BUILD @@ -17,9 +17,9 @@ go_test( "//testdata/stu3:examples", ], deps = [ - "//go/google/fhir/jsonformat", - "//go/google/fhir/jsonformat/internal/jsonpbhelper", - "//go/google/fhir/jsonformat/internal/protopath", + "//go/jsonformat", + "//go/jsonformat/internal/jsonpbhelper", + "//go/jsonformat/internal/protopath", "//proto/r4/core/resources:bundle_and_contained_resource_go_proto", "//proto/r4/core/resources:composition_go_proto", "//proto/r4/core/resources:observation_go_proto", @@ -46,7 +46,7 @@ go_test( ":testdata", ], deps = [ - "//go/google/fhir/jsonformat", + "//go/jsonformat", "@io_bazel_rules_go//go/tools/bazel:go_default_library", ], ) diff --git a/go/google/fhir/jsonformat/test/integration_test.go b/go/jsonformat/test/integration_test.go similarity index 99% rename from go/google/fhir/jsonformat/test/integration_test.go rename to go/jsonformat/test/integration_test.go index a1a53dcc8..d554003d2 100644 --- a/go/google/fhir/jsonformat/test/integration_test.go +++ b/go/jsonformat/test/integration_test.go @@ -28,9 +28,9 @@ import ( "testing" "github.com/bazelbuild/rules_go/go/tools/bazel" - "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper" - "google/fhir/jsonformat/internal/protopath/protopath" - "google/fhir/jsonformat/jsonformat" + "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper" + "github.com/google/fhir/go/jsonformat/internal/protopath" + "github.com/google/fhir/go/jsonformat" "github.com/google/go-cmp/cmp" "github.com/golang/protobuf/proto" "google.golang.org/protobuf/testing/protocmp" diff --git a/go/google/fhir/jsonformat/test/perf_test.go b/go/jsonformat/test/perf_test.go similarity index 98% rename from go/google/fhir/jsonformat/test/perf_test.go rename to go/jsonformat/test/perf_test.go index eb3acc708..78db4297e 100644 --- a/go/google/fhir/jsonformat/test/perf_test.go +++ b/go/jsonformat/test/perf_test.go @@ -22,7 +22,7 @@ import ( "testing" "github.com/bazelbuild/rules_go/go/tools/bazel" - "google/fhir/jsonformat/jsonformat" + "github.com/google/fhir/go/jsonformat" ) const ( diff --git a/go/google/fhir/jsonformat/test/testdata/synthea.bundle.json b/go/jsonformat/test/testdata/synthea.bundle.json similarity index 100% rename from go/google/fhir/jsonformat/test/testdata/synthea.bundle.json rename to go/jsonformat/test/testdata/synthea.bundle.json diff --git a/go/google/fhir/jsonformat/unmarshaller.go b/go/jsonformat/unmarshaller.go similarity index 99% rename from go/google/fhir/jsonformat/unmarshaller.go rename to go/jsonformat/unmarshaller.go index 0ec92c66f..5ae153393 100644 --- a/go/google/fhir/jsonformat/unmarshaller.go +++ b/go/jsonformat/unmarshaller.go @@ -25,8 +25,8 @@ import ( "time" "unicode/utf8" - "google/fhir/jsonformat/internal/accessor/accessor" - "google/fhir/jsonformat/internal/jsonpbhelper/jsonpbhelper" + "github.com/google/fhir/go/jsonformat/internal/accessor" + "github.com/google/fhir/go/jsonformat/internal/jsonpbhelper" "github.com/json-iterator/go" "github.com/golang/protobuf/proto" "github.com/golang/protobuf/ptypes" diff --git a/go/google/fhir/jsonformat/unmarshaller_test.go b/go/jsonformat/unmarshaller_test.go similarity index 100% rename from go/google/fhir/jsonformat/unmarshaller_test.go rename to go/jsonformat/unmarshaller_test.go diff --git a/go/google/fhir/jsonformat/version_config.go b/go/jsonformat/version_config.go similarity index 100% rename from go/google/fhir/jsonformat/version_config.go rename to go/jsonformat/version_config.go diff --git a/java/BUILD b/java/BUILD index 418382c79..59476872b 100644 --- a/java/BUILD +++ b/java/BUILD @@ -11,7 +11,7 @@ java_library( deps = [ ":common", "//proto:annotations_java_proto", - "//proto/r4:google_extensions_java_proto", + "//proto/r4:fhirproto_extensions_java_proto", "//proto/r4/core:datatypes_java_proto", "//proto/stu3:datatypes_java_proto", "@com_google_protobuf//:protobuf_java", @@ -189,10 +189,10 @@ java_library( ":proto_gen_transformer", ":resource_utils", "//proto:annotations_java_proto", + "//proto/r4:fhirproto_extensions_java_proto", "//proto/r4/core:datatypes_java_proto", "//proto/r4/core/resources:bundle_and_contained_resource_java_proto", "//proto/stu3:datatypes_java_proto", - "//proto/stu3:extensions_java_proto", "//proto/stu3:resources_java_proto", "@com_google_protobuf//:protobuf_java", "@maven//:com_google_code_gson_gson", @@ -369,7 +369,8 @@ java_test( deps = [ ":primitive_wrappers", "//proto/r4/core:datatypes_java_proto", - "//proto/stu3:extensions_java_proto", + "//proto/stu3:fhirproto_extensions_java_proto", + "//proto/stu3:ml_extensions_java_proto", "@bazel_tools//tools/java/runfiles", "@com_google_protobuf//:protobuf_java", "@maven//:com_google_guava_guava", @@ -712,7 +713,7 @@ java_test( ":validation_test_base", "//proto/stu3:codes_java_proto", "//proto/stu3:datatypes_java_proto", - "//proto/stu3:extensions_java_proto", + "//proto/stu3:fhirproto_extensions_java_proto", "//proto/stu3:uscore_java_proto", "@bazel_tools//tools/java/runfiles", "@com_google_protobuf//:protobuf_java", @@ -731,7 +732,7 @@ java_test( deps = [ ":json_format", ":validation_test_base", - "//proto/r4:google_extensions_java_proto", + "//proto/r4:fhirproto_extensions_java_proto", "//proto/r4:uscore_java_proto", "//proto/r4/core:datatypes_java_proto", "@bazel_tools//tools/java/runfiles", diff --git a/java/src/main/java/com/google/fhir/common/JsonFormat.java b/java/src/main/java/com/google/fhir/common/JsonFormat.java index 5770b1d9c..ec1296cb5 100644 --- a/java/src/main/java/com/google/fhir/common/JsonFormat.java +++ b/java/src/main/java/com/google/fhir/common/JsonFormat.java @@ -21,7 +21,7 @@ import com.google.fhir.proto.Annotations; import com.google.fhir.proto.Annotations.FhirVersion; import com.google.fhir.r4.core.Element; -import com.google.fhir.stu3.google.PrimitiveHasNoValue; +import com.google.fhir.r4.fhirproto.PrimitiveHasNoValue; import com.google.fhir.wrappers.CodeWrapper; import com.google.fhir.wrappers.ExtensionWrapper; import com.google.fhir.wrappers.PrimitiveWrapper; @@ -61,10 +61,9 @@ private enum FhirJsonFormat { private JsonFormat() {} - // TODO: Use r4 extension once generated. private static final PrimitiveHasNoValue PRIMITIVE_HAS_NO_VALUE = PrimitiveHasNoValue.newBuilder() - .setValueBoolean(com.google.fhir.stu3.proto.Boolean.newBuilder().setValue(true)) + .setValueBoolean(com.google.fhir.r4.core.Boolean.newBuilder().setValue(true)) .build(); private static boolean isPrimitiveType(FieldDescriptor field) { diff --git a/java/src/main/java/com/google/fhir/wrappers/Base64BinaryWrapper.java b/java/src/main/java/com/google/fhir/wrappers/Base64BinaryWrapper.java index 165666588..143e44a89 100644 --- a/java/src/main/java/com/google/fhir/wrappers/Base64BinaryWrapper.java +++ b/java/src/main/java/com/google/fhir/wrappers/Base64BinaryWrapper.java @@ -19,7 +19,7 @@ import com.google.fhir.common.ProtoUtils; import com.google.fhir.r4.core.Base64Binary; import com.google.fhir.r4.core.PositiveInt; -import com.google.fhir.r4.google.Base64BinarySeparatorStride; +import com.google.fhir.r4.fhirproto.Base64BinarySeparatorStride; import com.google.protobuf.ByteString; import com.google.protobuf.Message; import com.google.protobuf.MessageOrBuilder; diff --git a/java/src/main/java/com/google/fhir/wrappers/PrimitiveWrapper.java b/java/src/main/java/com/google/fhir/wrappers/PrimitiveWrapper.java index fc35675b0..0383ee567 100644 --- a/java/src/main/java/com/google/fhir/wrappers/PrimitiveWrapper.java +++ b/java/src/main/java/com/google/fhir/wrappers/PrimitiveWrapper.java @@ -19,7 +19,7 @@ import com.google.fhir.r4.core.Boolean; import com.google.fhir.r4.core.Element; import com.google.fhir.r4.core.Extension; -import com.google.fhir.r4.google.PrimitiveHasNoValue; +import com.google.fhir.r4.fhirproto.PrimitiveHasNoValue; import com.google.gson.JsonPrimitive; import com.google.protobuf.Descriptors.Descriptor; import com.google.protobuf.Descriptors.FieldDescriptor; diff --git a/java/src/test/java/com/google/fhir/r4/wrappers/ValidationTest.java b/java/src/test/java/com/google/fhir/r4/wrappers/ValidationTest.java index 3a18c4a46..9ab291b93 100644 --- a/java/src/test/java/com/google/fhir/r4/wrappers/ValidationTest.java +++ b/java/src/test/java/com/google/fhir/r4/wrappers/ValidationTest.java @@ -17,7 +17,7 @@ import com.google.devtools.build.runfiles.Runfiles; import com.google.fhir.common.JsonFormat; import com.google.fhir.r4.core.Boolean; -import com.google.fhir.r4.google.PrimitiveHasNoValue; +import com.google.fhir.r4.fhirproto.PrimitiveHasNoValue; import com.google.fhir.r4.uscore.UsCoreDirectEmail; import com.google.fhir.testing.ValidationTestBase; import com.google.protobuf.TextFormat; diff --git a/java/src/test/java/com/google/fhir/stu3/wrappers/ValidationTest.java b/java/src/test/java/com/google/fhir/stu3/wrappers/ValidationTest.java index b50bec806..2947b2eaf 100644 --- a/java/src/test/java/com/google/fhir/stu3/wrappers/ValidationTest.java +++ b/java/src/test/java/com/google/fhir/stu3/wrappers/ValidationTest.java @@ -16,7 +16,7 @@ import com.google.devtools.build.runfiles.Runfiles; import com.google.fhir.common.JsonFormat; -import com.google.fhir.stu3.google.PrimitiveHasNoValue; +import com.google.fhir.stu3.fhirproto.PrimitiveHasNoValue; import com.google.fhir.stu3.proto.Boolean; import com.google.fhir.stu3.uscore.UsCoreDirectEmail; import com.google.fhir.testing.ValidationTestBase; diff --git a/java/src/test/java/com/google/fhir/wrappers/ExtensionWrapperTest.java b/java/src/test/java/com/google/fhir/wrappers/ExtensionWrapperTest.java index f70c42145..3c5ac7cb1 100644 --- a/java/src/test/java/com/google/fhir/wrappers/ExtensionWrapperTest.java +++ b/java/src/test/java/com/google/fhir/wrappers/ExtensionWrapperTest.java @@ -19,9 +19,9 @@ import com.google.common.io.Files; import com.google.devtools.build.runfiles.Runfiles; import com.google.fhir.r4.core.Extension; -import com.google.fhir.stu3.google.EventLabel; -import com.google.fhir.stu3.google.EventTrigger; -import com.google.fhir.stu3.google.PrimitiveHasNoValue; +import com.google.fhir.stu3.fhirproto.PrimitiveHasNoValue; +import com.google.fhir.stu3.ml.EventLabel; +import com.google.fhir.stu3.ml.EventTrigger; import com.google.protobuf.Message; import com.google.protobuf.TextFormat; import java.io.File; diff --git a/proto/r4/BUILD b/proto/r4/BUILD index 51f8cf4b6..c26bf11b5 100644 --- a/proto/r4/BUILD +++ b/proto/r4/BUILD @@ -11,14 +11,26 @@ exports_files(["version_config.textproto"]) fhir_proto_library( srcs = [ - "google_extensions.proto", + "fhirproto_extensions.proto", ], proto_deps = [ "//proto:annotations_proto", "//proto/r4/core:codes_proto", "//proto/r4/core:datatypes_proto", ], - proto_library_prefix = "google_extensions", + proto_library_prefix = "fhirproto_extensions", +) + +fhir_proto_library( + srcs = [ + "ml_extensions.proto", + ], + proto_deps = [ + "//proto:annotations_proto", + "//proto/r4/core:codes_proto", + "//proto/r4/core:datatypes_proto", + ], + proto_library_prefix = "ml_extensions", ) gen_fhir_protos( diff --git a/proto/r4/fhirproto_extensions.proto b/proto/r4/fhirproto_extensions.proto new file mode 100755 index 000000000..3f29f6a72 --- /dev/null +++ b/proto/r4/fhirproto_extensions.proto @@ -0,0 +1,63 @@ +// Copyright 2019 Google Inc. +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// https://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +syntax = "proto3"; + +package google.fhir.r4.fhirproto; + +import "proto/annotations.proto"; +import "proto/r4/core/datatypes.proto"; + +option java_multiple_files = true; +option java_package = "com.google.fhir.r4.fhirproto"; +option (.google.fhir.proto.fhir_version) = R4; + +// Auto-generated from StructureDefinition for PrimitiveHasNoValue. +// Whether or not the primitive is missing a value. +// See https://g.co/fhir/StructureDefinition/primitiveHasNoValue +message PrimitiveHasNoValue { + option (.google.fhir.proto.structure_definition_kind) = KIND_COMPLEX_TYPE; + option (.google.fhir.proto.fhir_profile_base) = + "http://hl7.org/fhir/StructureDefinition/Extension"; + option (.google.fhir.proto.fhir_structure_definition_url) = + "https://g.co/fhir/StructureDefinition/primitiveHasNoValue"; + + // Unique id for inter-element referencing + core.String id = 1; + + // Value of extension + core.Boolean value_boolean = 3; +} + +// Auto-generated from StructureDefinition for Base64BinarySeparatorStride. +// Base64Binary rendering parameters. +// See https://g.co/fhir/StructureDefinition/base64Binary-separatorStride +message Base64BinarySeparatorStride { + option (.google.fhir.proto.structure_definition_kind) = KIND_COMPLEX_TYPE; + option (.google.fhir.proto.fhir_profile_base) = + "http://hl7.org/fhir/StructureDefinition/Extension"; + option (.google.fhir.proto.fhir_structure_definition_url) = + "https://g.co/fhir/StructureDefinition/base64Binary-separatorStride"; + + // Unique id for inter-element referencing + core.String id = 1; + + // The separator, usually a sequence of spaces. + core.String separator = 4 + [(.google.fhir.proto.validation_requirement) = REQUIRED_BY_FHIR]; + + // The stride. + core.PositiveInt stride = 5 + [(.google.fhir.proto.validation_requirement) = REQUIRED_BY_FHIR]; +} diff --git a/proto/r4/google_extensions.proto b/proto/r4/ml_extensions.proto similarity index 70% rename from proto/r4/google_extensions.proto rename to proto/r4/ml_extensions.proto index df02cf0d4..534b63956 100755 --- a/proto/r4/google_extensions.proto +++ b/proto/r4/ml_extensions.proto @@ -14,54 +14,15 @@ syntax = "proto3"; -package google.fhir.r4.google; +package google.fhir.r4.ml; import "proto/annotations.proto"; import "proto/r4/core/datatypes.proto"; option java_multiple_files = true; -option java_package = "com.google.fhir.r4.google"; +option java_package = "com.google.fhir.r4.ml"; option (.google.fhir.proto.fhir_version) = R4; -// Auto-generated from StructureDefinition for PrimitiveHasNoValue. -// Whether or not the primitive is missing a value. -// See https://g.co/fhir/StructureDefinition/primitiveHasNoValue -message PrimitiveHasNoValue { - option (.google.fhir.proto.structure_definition_kind) = KIND_COMPLEX_TYPE; - option (.google.fhir.proto.fhir_profile_base) = - "http://hl7.org/fhir/StructureDefinition/Extension"; - option (.google.fhir.proto.fhir_structure_definition_url) = - "https://g.co/fhir/StructureDefinition/primitiveHasNoValue"; - - // Unique id for inter-element referencing - core.String id = 1; - - // Value of extension - core.Boolean value_boolean = 3; -} - -// Auto-generated from StructureDefinition for Base64BinarySeparatorStride. -// Base64Binary rendering parameters. -// See https://g.co/fhir/StructureDefinition/base64Binary-separatorStride -message Base64BinarySeparatorStride { - option (.google.fhir.proto.structure_definition_kind) = KIND_COMPLEX_TYPE; - option (.google.fhir.proto.fhir_profile_base) = - "http://hl7.org/fhir/StructureDefinition/Extension"; - option (.google.fhir.proto.fhir_structure_definition_url) = - "https://g.co/fhir/StructureDefinition/base64Binary-separatorStride"; - - // Unique id for inter-element referencing - core.String id = 1; - - // The separator, usually a sequence of spaces. - core.String separator = 4 - [(.google.fhir.proto.validation_requirement) = REQUIRED_BY_FHIR]; - - // The stride. - core.PositiveInt stride = 5 - [(.google.fhir.proto.validation_requirement) = REQUIRED_BY_FHIR]; -} - // Auto-generated from StructureDefinition for EventLabel. // EventLabels define labels used for TensorFlow model training and evaluation. // See https://g.co/fhir/StructureDefinition/eventLabel diff --git a/proto/stu3/BUILD b/proto/stu3/BUILD index 90a1f1b16..302d275d5 100644 --- a/proto/stu3/BUILD +++ b/proto/stu3/BUILD @@ -37,7 +37,6 @@ fhir_proto_library( fhir_proto_library( srcs = [ "extensions.proto", - "google_extensions.proto", ], proto_deps = [ ":codes_proto", @@ -47,6 +46,30 @@ fhir_proto_library( proto_library_prefix = "extensions", ) +fhir_proto_library( + srcs = [ + "fhirproto_extensions.proto", + ], + proto_deps = [ + ":codes_proto", + ":datatypes_proto", + "//proto:annotations_proto", + ], + proto_library_prefix = "fhirproto_extensions", +) + +fhir_proto_library( + srcs = [ + "ml_extensions.proto", + ], + proto_deps = [ + ":codes_proto", + ":datatypes_proto", + "//proto:annotations_proto", + ], + proto_library_prefix = "ml_extensions", +) + fhir_proto_library( srcs = [ "resources.proto", diff --git a/proto/stu3/fhirproto_extensions.proto b/proto/stu3/fhirproto_extensions.proto new file mode 100755 index 000000000..f3821e854 --- /dev/null +++ b/proto/stu3/fhirproto_extensions.proto @@ -0,0 +1,68 @@ +// Copyright 2018 Google Inc. +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// https://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +syntax = "proto3"; + +package google.fhir.stu3.fhirproto; + +import "proto/annotations.proto"; +import "proto/stu3/datatypes.proto"; + +option java_multiple_files = true; +option java_package = "com.google.fhir.stu3.fhirproto"; +option go_package = "google/fhir/stu3/proto"; +option (.google.fhir.proto.fhir_version) = STU3; + +// Whether or not the primitive is missing a value. +// See https://g.co/fhir/StructureDefinition/primitiveHasNoValue +message PrimitiveHasNoValue { + option (.google.fhir.proto.structure_definition_kind) = KIND_COMPLEX_TYPE; + option (.google.fhir.proto.fhir_profile_base) = + "http://hl7.org/fhir/StructureDefinition/Extension"; + option (.google.fhir.proto.fhir_structure_definition_url) = + "https://g.co/fhir/StructureDefinition/primitiveHasNoValue"; + + // xml:id (or equivalent in JSON) + proto.String id = 1; + + // Value of extension + proto.Boolean value_boolean = 3; +} + +// Base64Binary rendering parameters. +// See https://g.co/fhir/StructureDefinition/base64Binary-separatorStride +message Base64BinarySeparatorStride { + option (.google.fhir.proto.structure_definition_kind) = KIND_COMPLEX_TYPE; + option (.google.fhir.proto.fhir_profile_base) = + "http://hl7.org/fhir/StructureDefinition/Extension"; + option (.google.fhir.proto.fhir_structure_definition_url) = + "https://g.co/fhir/StructureDefinition/base64Binary-separatorStride"; + + // xml:id (or equivalent in JSON) + proto.String id = 1; + + // The separator, usually a sequence of spaces. + proto.String separator = 4 [ + (.google.fhir.proto.validation_requirement) = REQUIRED_BY_FHIR, + (.google.fhir.proto.fhir_path_constraint) = + "extension.exists() != value.exists()" + ]; + + // The stride. + proto.PositiveInt stride = 5 [ + (.google.fhir.proto.validation_requirement) = REQUIRED_BY_FHIR, + (.google.fhir.proto.fhir_path_constraint) = + "extension.exists() != value.exists()" + ]; +} diff --git a/proto/stu3/google_extensions.proto b/proto/stu3/ml_extensions.proto similarity index 73% rename from proto/stu3/google_extensions.proto rename to proto/stu3/ml_extensions.proto index c7051ccbf..e1d0749df 100755 --- a/proto/stu3/google_extensions.proto +++ b/proto/stu3/ml_extensions.proto @@ -14,61 +14,16 @@ syntax = "proto3"; -package google.fhir.stu3.google; +package google.fhir.stu3.ml; import "proto/annotations.proto"; import "proto/stu3/datatypes.proto"; option java_multiple_files = true; -option java_package = "com.google.fhir.stu3.google"; +option java_package = "com.google.fhir.stu3.ml"; option go_package = "google/fhir/stu3/proto"; option (.google.fhir.proto.fhir_version) = STU3; -// Auto-generated from StructureDefinition for PrimitiveHasNoValue. -// Whether or not the primitive is missing a value. -// See https://g.co/fhir/StructureDefinition/primitiveHasNoValue -message PrimitiveHasNoValue { - option (.google.fhir.proto.structure_definition_kind) = KIND_COMPLEX_TYPE; - option (.google.fhir.proto.fhir_profile_base) = - "http://hl7.org/fhir/StructureDefinition/Extension"; - option (.google.fhir.proto.fhir_structure_definition_url) = - "https://g.co/fhir/StructureDefinition/primitiveHasNoValue"; - - // xml:id (or equivalent in JSON) - proto.String id = 1; - - // Value of extension - proto.Boolean value_boolean = 3; -} - -// Auto-generated from StructureDefinition for Base64BinarySeparatorStride. -// Base64Binary rendering parameters. -// See https://g.co/fhir/StructureDefinition/base64Binary-separatorStride -message Base64BinarySeparatorStride { - option (.google.fhir.proto.structure_definition_kind) = KIND_COMPLEX_TYPE; - option (.google.fhir.proto.fhir_profile_base) = - "http://hl7.org/fhir/StructureDefinition/Extension"; - option (.google.fhir.proto.fhir_structure_definition_url) = - "https://g.co/fhir/StructureDefinition/base64Binary-separatorStride"; - - // xml:id (or equivalent in JSON) - proto.String id = 1; - - // The separator, usually a sequence of spaces. - proto.String separator = 4 [ - (.google.fhir.proto.validation_requirement) = REQUIRED_BY_FHIR, - (.google.fhir.proto.fhir_path_constraint) = - "extension.exists() != value.exists()" - ]; - - // The stride. - proto.PositiveInt stride = 5 [ - (.google.fhir.proto.validation_requirement) = REQUIRED_BY_FHIR, - (.google.fhir.proto.fhir_path_constraint) = - "extension.exists() != value.exists()" - ]; -} - // Auto-generated from StructureDefinition for EventLabel. // EventLabels define labels used for TensorFlow model training and evaluation. // See https://g.co/fhir/StructureDefinition/eventLabel diff --git a/py/google/fhir/labels/BUILD b/py/google/fhir/labels/BUILD index c6c0081e4..28e2b3485 100644 --- a/py/google/fhir/labels/BUILD +++ b/py/google/fhir/labels/BUILD @@ -56,7 +56,7 @@ py_library( deps = [ ":encounter", "//proto/stu3:datatypes_py_pb2", - "//proto/stu3:extensions_py_pb2", + "//proto/stu3:ml_extensions_py_pb2", "//proto/stu3:resources_py_pb2", ], ) @@ -97,11 +97,10 @@ py_library( deps = [ ":encounter", ":label", - "//proto/stu3:extensions_py_pb2", + "//proto/stu3:ml_extensions_py_pb2", "//proto/stu3:resources_py_pb2", "@absl_py//absl:app", "@absl_py//absl/flags", - "@absl_py//absl/logging", requirement("apache_beam"), ], ) diff --git a/py/google/fhir/labels/bundle_to_label.py b/py/google/fhir/labels/bundle_to_label.py index 333b835d6..fff92f9f9 100644 --- a/py/google/fhir/labels/bundle_to_label.py +++ b/py/google/fhir/labels/bundle_to_label.py @@ -21,7 +21,7 @@ import apache_beam as beam from apache_beam.options import pipeline_options -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 from proto.stu3 import resources_pb2 from py.google.fhir.labels import encounter from py.google.fhir.labels import label @@ -45,7 +45,7 @@ @beam.typehints.with_input_types(resources_pb2.Bundle) -@beam.typehints.with_output_types(google_extensions_pb2.EventLabel) +@beam.typehints.with_output_types(ml_extensions_pb2.EventLabel) class LengthOfStayRangeLabelAt24HoursFn(beam.DoFn): """Converts Bundle into length of stay range at 24 hours label. @@ -58,8 +58,8 @@ def __init__(self, for_synthea: bool = False): self._for_synthea = for_synthea def process( - self, bundle: resources_pb2.Bundle - ) -> Iterator[google_extensions_pb2.EventLabel]: + self, + bundle: resources_pb2.Bundle) -> Iterator[ml_extensions_pb2.EventLabel]: """Iterate through bundle and yield label. Args: @@ -111,7 +111,7 @@ def main(argv: List[str]): LengthOfStayRangeLabelAt24HoursFn(for_synthea=flags.FLAGS.for_synthea)) _ = labels | beam.io.WriteToTFRecord( flags.FLAGS.output_path, - coder=beam.coders.ProtoCoder(google_extensions_pb2.EventLabel), + coder=beam.coders.ProtoCoder(ml_extensions_pb2.EventLabel), file_name_suffix='.tfrecords') p.run() diff --git a/py/google/fhir/labels/label.py b/py/google/fhir/labels/label.py index f25be7c98..29c2c3f6c 100644 --- a/py/google/fhir/labels/label.py +++ b/py/google/fhir/labels/label.py @@ -31,7 +31,7 @@ from typing import Iterator, Optional from proto.stu3 import datatypes_pb2 -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 from proto.stu3 import resources_pb2 from py.google.fhir.labels import encounter @@ -60,10 +60,9 @@ def ToMicroSeconds(dt: datetime.datetime) -> int: # Note: this API only compose encounter level API. -def ComposeLabel( - patient: resources_pb2.Patient, enc: resources_pb2.Encounter, - label_name: str, label_val: str, - label_time: datetime.datetime) -> google_extensions_pb2.EventLabel: +def ComposeLabel(patient: resources_pb2.Patient, enc: resources_pb2.Encounter, + label_name: str, label_val: str, + label_time: datetime.datetime) -> ml_extensions_pb2.EventLabel: """Compose an event_label proto given inputs. Args: @@ -76,7 +75,7 @@ def ComposeLabel( Returns: event_label proto. """ - event_label = google_extensions_pb2.EventLabel() + event_label = ml_extensions_pb2.EventLabel() # set patient_id event_label.patient.patient_id.value = patient.id.value event_label.type.system.value = GOOGLE_FHIR_LABEL_SYTEM @@ -84,7 +83,7 @@ def ComposeLabel( event_label.event_time.value_us = ToMicroSeconds(label_time) event_label.source.encounter_id.value = enc.id.value - label = google_extensions_pb2.EventLabel.Label() + label = ml_extensions_pb2.EventLabel.Label() label.class_name.system.value = GOOGLE_FHIR_LABEL_SYTEM label.class_name.code.value = label_val event_label.label.add().CopyFrom(label) @@ -94,7 +93,7 @@ def ComposeLabel( def LengthOfStayRangeAt24Hours( patient: resources_pb2.Patient, - enc: resources_pb2.Encounter) -> Iterator[google_extensions_pb2.EventLabel]: + enc: resources_pb2.Encounter) -> Iterator[ml_extensions_pb2.EventLabel]: """Generate length of stay range labels at 24 hours after admission. Args: @@ -102,7 +101,7 @@ def LengthOfStayRangeAt24Hours( enc: encounter, caller needs to do the proper cohort filterings. Yields: - An instance of google_extensions_pb2.EventLabel. + An instance of ml_extensions_pb2.EventLabel. """ label_time = encounter.AtDuration(enc, 24) ecounter_length_days = encounter.EncounterLengthDays(enc) diff --git a/py/google/fhir/labels/label_test.py b/py/google/fhir/labels/label_test.py index 927eaba78..ca4048a4b 100644 --- a/py/google/fhir/labels/label_test.py +++ b/py/google/fhir/labels/label_test.py @@ -22,7 +22,7 @@ from absl.testing import parameterized from google.protobuf import text_format from proto.stu3 import datatypes_pb2 -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 from proto.stu3 import resources_pb2 from py.google.fhir.labels import label @@ -42,7 +42,7 @@ def setUp(self): self._patient = resources_pb2.Patient() self._patient.id.value = 'Patient/1' - self._expected_label = google_extensions_pb2.EventLabel() + self._expected_label = ml_extensions_pb2.EventLabel() with open(os.path.join(self._test_data_dir, 'label_1.pbtxt')) as f: text_format.Parse(f.read(), self._expected_label) diff --git a/py/google/fhir/seqex/BUILD b/py/google/fhir/seqex/BUILD index d504298a3..4cd8d0a97 100644 --- a/py/google/fhir/seqex/BUILD +++ b/py/google/fhir/seqex/BUILD @@ -33,7 +33,7 @@ pyx_library( "//cc/google/fhir/seqex:stu3", "//cc/google/fhir/seqex:text_tokenizer", "//proto:version_config_cc_proto", - "//proto/stu3:extensions_cc_proto", + "//proto/stu3:ml_extensions_cc_proto", "//proto/stu3:resources_cc_proto", "@org_tensorflow//tensorflow/core:protos_all_cc", ], @@ -49,7 +49,7 @@ py_test( deps = [ ":bundle_seqex_converter", "//proto:version_config_py_pb2", - "//proto/stu3:extensions_py_pb2", + "//proto/stu3:ml_extensions_py_pb2", "//proto/stu3:resources_py_pb2", "//py/google/fhir/testutil:protobuf_compare", "@absl_py//absl/flags", @@ -66,12 +66,12 @@ pyx_library( "bundle_to_seqex_util.pyx", ], py_deps = [ - "//proto/stu3:extensions_py_pb2", + "//proto/stu3:ml_extensions_py_pb2", ], srcs_version = "PY3ONLY", deps = [ "//cc/google/fhir/seqex:stu3", - "//proto/stu3:extensions_cc_proto", + "//proto/stu3:ml_extensions_cc_proto", "//proto/stu3:resources_cc_proto", ], ) @@ -82,7 +82,7 @@ py_test( python_version = "PY3", deps = [ ":bundle_to_seqex_util", - "//proto/stu3:extensions_py_pb2", + "//proto/stu3:ml_extensions_py_pb2", "//proto/stu3:resources_py_pb2", "//py/google/fhir/testutil:protobuf_compare", "@absl_py//absl/testing:absltest", @@ -99,7 +99,7 @@ py_library( deps = [ ":bundle_seqex_converter", ":bundle_to_seqex_util", - "//proto/stu3:extensions_py_pb2", + "//proto/stu3:ml_extensions_py_pb2", "//proto/stu3:resources_py_pb2", "//py/google/fhir/stu3:util", "@org_tensorflow//tensorflow/core:protos_all_py", @@ -120,7 +120,7 @@ py_test( ":bundle_to_seqex", ":bundle_seqex_converter", "@com_google_protobuf//:protobuf_python", - "//proto/stu3:extensions_py_pb2", + "//proto/stu3:ml_extensions_py_pb2", "//proto/stu3:resources_py_pb2", "//proto:version_config_py_pb2", "//py/google/fhir/testutil:protobuf_compare", @@ -142,12 +142,11 @@ py_binary( deps = [ ":bundle_to_seqex", "@com_google_protobuf//:protobuf_python", - "//proto/stu3:extensions_py_pb2", + "//proto/stu3:ml_extensions_py_pb2", "//proto/stu3:resources_py_pb2", "//proto:version_config_py_pb2", "@absl_py//absl:app", "@absl_py//absl/flags", - "@absl_py//absl/logging", "@org_tensorflow//tensorflow/core:protos_all_py", requirement("apache_beam"), ], diff --git a/py/google/fhir/seqex/bundle_to_seqex.py b/py/google/fhir/seqex/bundle_to_seqex.py index 59a23c14b..58fdf7c10 100644 --- a/py/google/fhir/seqex/bundle_to_seqex.py +++ b/py/google/fhir/seqex/bundle_to_seqex.py @@ -17,7 +17,7 @@ import apache_beam as beam -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 from proto.stu3 import resources_pb2 from py.google.fhir.seqex import bundle_to_seqex_converter from py.google.fhir.seqex import bundle_to_seqex_util @@ -28,9 +28,8 @@ _BUNDLE_TAG = "bundle" _TRIGGERS_TAG = "trigger_labels_pair_lists" -typehints_trigger_labels_pair_list = beam.typehints.List[ - beam.typehints.Tuple[google_extensions_pb2.EventTrigger, beam.typehints - .List[beam.typehints.Any]]] +typehints_trigger_labels_pair_list = beam.typehints.List[beam.typehints.Tuple[ + ml_extensions_pb2.EventTrigger, beam.typehints.List[beam.typehints.Any]]] @beam.typehints.with_input_types(resources_pb2.Bundle) @@ -48,9 +47,9 @@ def process(self, bundle): yield (("Patient/" + patient.id.value).encode("utf-8"), bundle) -@beam.typehints.with_input_types(google_extensions_pb2.EventLabel) +@beam.typehints.with_input_types(ml_extensions_pb2.EventLabel) @beam.typehints.with_output_types( - beam.typehints.Tuple[bytes, google_extensions_pb2.EventLabel]) + beam.typehints.Tuple[bytes, ml_extensions_pb2.EventLabel]) class KeyEventLabelByPatientIdFn(beam.DoFn): """Key EventLabel by patient id.""" diff --git a/py/google/fhir/seqex/bundle_to_seqex_converter.pxd b/py/google/fhir/seqex/bundle_to_seqex_converter.pxd index 9747e0a4d..8107440e0 100644 --- a/py/google/fhir/seqex/bundle_to_seqex_converter.pxd +++ b/py/google/fhir/seqex/bundle_to_seqex_converter.pxd @@ -27,12 +27,12 @@ cdef extern from "tensorflow/core/example/example.pb.h" namespace "tensorflow" n bool ParseFromString(const string& input) string SerializeAsString() const -cdef extern from "proto/stu3/google_extensions.pb.h" namespace "google::fhir::stu3::google" nogil: +cdef extern from "proto/stu3/ml_extensions.pb.h" namespace "google::fhir::stu3::ml" nogil: cdef cppclass EventTrigger: bool ParseFromString(const string& input) pass -cdef extern from "proto/stu3/google_extensions.pb.h" namespace "google::fhir::stu3::google" nogil: +cdef extern from "proto/stu3/ml_extensions.pb.h" namespace "google::fhir::stu3::ml" nogil: cdef cppclass EventLabel: bool ParseFromString(const string& input) pass diff --git a/py/google/fhir/seqex/bundle_to_seqex_converter_test.py b/py/google/fhir/seqex/bundle_to_seqex_converter_test.py index 4d7acaa1f..6701fabb0 100644 --- a/py/google/fhir/seqex/bundle_to_seqex_converter_test.py +++ b/py/google/fhir/seqex/bundle_to_seqex_converter_test.py @@ -22,7 +22,7 @@ from absl.testing import absltest from google.protobuf import text_format from proto import version_config_pb2 -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 from proto.stu3 import resources_pb2 from py.google.fhir.seqex import bundle_to_seqex_converter from py.google.fhir.testutil import protobuf_compare @@ -42,12 +42,12 @@ def setUp(self): self._version_config = text_format.Parse( f.read(), version_config_pb2.VersionConfig()) - def _runTest( - self, patient_key: bytes, bundle: resources_pb2.Bundle, - event_trigger_labels_list: Tuple[google_extensions_pb2.EventTrigger, - List[Any]], - expected_outcomes: Tuple[Tuple[bytes, example_pb2.SequenceExample, int], - Any]): + def _runTest(self, patient_key: bytes, bundle: resources_pb2.Bundle, + event_trigger_labels_list: Tuple[ml_extensions_pb2.EventTrigger, + List[Any]], + expected_outcomes: Tuple[Tuple[bytes, + example_pb2.SequenceExample, int], + Any]): converter = bundle_to_seqex_converter.PyBundleToSeqexConverter( self._version_config, False, False) (begin_result, stats) = converter.begin(patient_key, bundle, @@ -71,7 +71,7 @@ def testSingleTriggerAndStats(self): event_trigger = text_format.Parse( """ event_time { value_us: 1420102800000000 } - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) event_trigger_labels = (event_trigger, list()) event_trigger_labels_list = (event_trigger_labels,) @@ -161,7 +161,7 @@ def testSingleTriggerAndLabel(self): """ event_time { value_us: 1420102800000000 } source { encounter_id { value: "1" } } - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) event_label = text_format.Parse( """ patient { patient_id { value: "14" } } @@ -174,7 +174,7 @@ def testSingleTriggerAndLabel(self): code { value: "red" } } } - """, google_extensions_pb2.EventLabel()) + """, ml_extensions_pb2.EventLabel()) event_trigger_labels = ( event_trigger, (event_label,), @@ -341,12 +341,12 @@ def testMultipleTriggersAndExamples(self): """ event_time { value_us: 1417424400000000 } source { encounter_id { value: "1" } } - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) event_trigger2 = text_format.Parse( """ event_time { value_us: 1420102800000000 } source { encounter_id { value: "2" } } - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) event_trigger_labels1 = ( event_trigger1, list(), diff --git a/py/google/fhir/seqex/bundle_to_seqex_main.py b/py/google/fhir/seqex/bundle_to_seqex_main.py index 782adc36a..ad8d6f8f2 100644 --- a/py/google/fhir/seqex/bundle_to_seqex_main.py +++ b/py/google/fhir/seqex/bundle_to_seqex_main.py @@ -26,7 +26,7 @@ from google.protobuf import text_format from proto import version_config_pb2 -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 from proto.stu3 import resources_pb2 from py.google.fhir.seqex import bundle_to_seqex from tensorflow.core.example import example_pb2 @@ -68,7 +68,7 @@ def main(argv: List[str]): event_labels = ( p | 'readEventLabels' >> beam.io.ReadFromTFRecord( FLAGS.label_path, - coder=beam.coders.ProtoCoder(google_extensions_pb2.EventLabel))) + coder=beam.coders.ProtoCoder(ml_extensions_pb2.EventLabel))) keyed_event_labels = bundle_to_seqex.CreateTriggerLabelsPairLists( event_labels) bundles_and_labels = bundle_to_seqex.CreateBundleAndLabels( diff --git a/py/google/fhir/seqex/bundle_to_seqex_test.py b/py/google/fhir/seqex/bundle_to_seqex_test.py index 67f5f392d..c5df73ab4 100644 --- a/py/google/fhir/seqex/bundle_to_seqex_test.py +++ b/py/google/fhir/seqex/bundle_to_seqex_test.py @@ -23,7 +23,7 @@ from apache_beam.testing import util from google.protobuf import text_format from proto import version_config_pb2 -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 from proto.stu3 import resources_pb2 from py.google.fhir.seqex import bundle_to_seqex from py.google.fhir.testutil import protobuf_compare @@ -77,7 +77,7 @@ def testKeyEventLabelByPatientIdFn(self): system { value: "urn:test:label" } code { value: "green" } } } - """, google_extensions_pb2.EventLabel()) + """, ml_extensions_pb2.EventLabel()) with test_pipeline.TestPipeline() as p: result = ( p @@ -102,18 +102,18 @@ def testCreateTriggerLabelsPairLists(self): """ event_time { value_us: 1417392000000000 } # "2014-12-01T00:00:00+00:00" source { encounter_id { value: "1" } } - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) trigger2 = text_format.Parse( """ event_time { value_us: 1417428000000000 } # "2014-12-01T01:00:00+00:00" - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) label1 = text_format.Parse( """ patient { patient_id { value: "14" } } type { code { value: "test1" } } event_time { value_us: 1417392000000000 } # "2014-12-01T00:00:00+00:00" source { encounter_id { value: "1" } } - """, google_extensions_pb2.EventLabel()) + """, ml_extensions_pb2.EventLabel()) label2 = text_format.Parse( """ patient { patient_id { value: "14" } } @@ -123,7 +123,7 @@ def testCreateTriggerLabelsPairLists(self): system { value: "urn:test:label" } code { value: "green" } } } - """, google_extensions_pb2.EventLabel()) + """, ml_extensions_pb2.EventLabel()) with test_pipeline.TestPipeline() as p: event_labels_pcoll = ( p | "CreateEventLabels" >> beam.Create([label1, label2])) @@ -176,13 +176,13 @@ def testCreateBundleAndLabels(self): bundle1_event_trigger = text_format.Parse( """ event_time { value_us: 1388566800000000 } # "2014-01-01T09:00:00+00:00" - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) # For the purpose of testing, bundle2 does not exist. bundle2_event_trigger = text_format.Parse( """ event_time { value_us: 1388566800000000 } # "2014-01-01T09:00:00+00:00" - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) bundle3 = text_format.Parse( """ @@ -235,12 +235,12 @@ def testBundleAndLabelsToSeqexDoFn(self): """ event_time { value_us: 1417424400000000 } source { encounter_id { value: "1" } } - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) event_trigger2 = text_format.Parse( """ event_time { value_us: 1420102800000000 } source { encounter_id { value: "2" } } - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) event_trigger_labels1 = ( event_trigger1, list(), diff --git a/py/google/fhir/seqex/bundle_to_seqex_util.pxd b/py/google/fhir/seqex/bundle_to_seqex_util.pxd index 44c469f17..83a7540b2 100644 --- a/py/google/fhir/seqex/bundle_to_seqex_util.pxd +++ b/py/google/fhir/seqex/bundle_to_seqex_util.pxd @@ -20,13 +20,13 @@ from libcpp.utility cimport pair from libcpp.string cimport string -cdef extern from "proto/stu3/google_extensions.pb.h" namespace "google::fhir::stu3::google" nogil: +cdef extern from "proto/stu3/ml_extensions.pb.h" namespace "google::fhir::stu3::ml" nogil: cdef cppclass EventLabel: bool ParseFromString(const string& input) string SerializeAsString() const pass -cdef extern from "proto/stu3/google_extensions.pb.h" namespace "google::fhir::stu3::google" nogil: +cdef extern from "proto/stu3/ml_extensions.pb.h" namespace "google::fhir::stu3::ml" nogil: cdef cppclass EventTrigger: bool ParseFromString(const string& input) string SerializeAsString() const diff --git a/py/google/fhir/seqex/bundle_to_seqex_util.pyx b/py/google/fhir/seqex/bundle_to_seqex_util.pyx index 01dd71949..f8f9df791 100644 --- a/py/google/fhir/seqex/bundle_to_seqex_util.pyx +++ b/py/google/fhir/seqex/bundle_to_seqex_util.pyx @@ -13,7 +13,7 @@ # See the License for the specific language governing permissions and # limitations under the License. -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 def get_trigger_labels_from_input_labels(event_label_list): @@ -37,10 +37,10 @@ def get_trigger_labels_from_input_labels(event_label_list): for c_trigger_labels_pair in c_trigger_labels_pair_vector: c_trigger_event = c_trigger_labels_pair.first c_event_label_vector = c_trigger_labels_pair.second - trigger_event = google_extensions_pb2.EventTrigger().FromString( + trigger_event = ml_extensions_pb2.EventTrigger().FromString( c_trigger_event.SerializeAsString()) event_label_list = [ - google_extensions_pb2.EventLabel().FromString( + ml_extensions_pb2.EventLabel().FromString( c_event_label.SerializeAsString()) for c_event_label in c_event_label_vector ] trigger_labels_tuple_list.append((trigger_event, event_label_list)) @@ -71,10 +71,10 @@ def get_trigger_labels_pair(bundle, label_names, trigger_event_name): for c_trigger_labels_pair in c_trigger_labels_pair_vector: c_trigger_event = c_trigger_labels_pair.first c_event_label_vector = c_trigger_labels_pair.second - trigger_event = google_extensions_pb2.EventTrigger().FromString( + trigger_event = ml_extensions_pb2.EventTrigger().FromString( c_trigger_event.SerializeAsString()) event_label_list = [ - google_extensions_pb2.EventLabel().FromString( + ml_extensions_pb2.EventLabel().FromString( c_event_label.SerializeAsString()) for c_event_label in c_event_label_vector ] trigger_labels_tuple_list.append((trigger_event, event_label_list)) diff --git a/py/google/fhir/seqex/bundle_to_seqex_util_test.py b/py/google/fhir/seqex/bundle_to_seqex_util_test.py index fdc51218f..c22c193a0 100644 --- a/py/google/fhir/seqex/bundle_to_seqex_util_test.py +++ b/py/google/fhir/seqex/bundle_to_seqex_util_test.py @@ -17,7 +17,7 @@ from absl.testing import absltest from google.protobuf import text_format -from proto.stu3 import google_extensions_pb2 +from proto.stu3 import ml_extensions_pb2 from proto.stu3 import resources_pb2 from py.google.fhir.seqex import bundle_to_seqex_util from py.google.fhir.testutil import protobuf_compare @@ -31,18 +31,18 @@ def test_get_trigger_labels_from_input_labels(self): """ event_time { value_us: 1417392000000000 } # "2014-12-01T00:00:00+00:00" source { encounter_id { value: "1" } } - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) trigger2 = text_format.Parse( """ event_time { value_us: 1417428000000000 } # "2014-12-01T01:00:00+00:00" - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) label1 = text_format.Parse( """ patient { patient_id { value: "14" } } type { code { value: "test1" } } event_time { value_us: 1417392000000000 } # "2014-12-01T00:00:00+00:00" source { encounter_id { value: "1" } } - """, google_extensions_pb2.EventLabel()) + """, ml_extensions_pb2.EventLabel()) label2 = text_format.Parse( """ patient { patient_id { value: "14" } } @@ -52,7 +52,7 @@ def test_get_trigger_labels_from_input_labels(self): system { value: "urn:test:label" } code { value: "green " } } } - """, google_extensions_pb2.EventLabel()) + """, ml_extensions_pb2.EventLabel()) got_list = bundle_to_seqex_util.get_trigger_labels_from_input_labels( [label1, label2]) self.assertLen(got_list, 2) @@ -160,7 +160,7 @@ def test_get_trigger_labels_pair(self): code { value: "at_discharge" } } event_time { value_us: 1388566800000000 } # "2014-01-01T09:00:00+00:00" - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) trigger2 = text_format.Parse( """ type { @@ -168,7 +168,7 @@ def test_get_trigger_labels_pair(self): code { value: "at_discharge" } } event_time { value_us: 1420102800000000 } # "2015-01-01T09:00:00+00:00" - """, google_extensions_pb2.EventTrigger()) + """, ml_extensions_pb2.EventTrigger()) label1 = text_format.Parse( """ type { @@ -177,7 +177,7 @@ def test_get_trigger_labels_pair(self): } event_time { value_us: 1388566800000000 } source { encounter_id { value: "1" } } - """, google_extensions_pb2.EventLabel()) + """, ml_extensions_pb2.EventLabel()) label2 = text_format.Parse( """ type { @@ -191,7 +191,7 @@ def test_get_trigger_labels_pair(self): code { value: "red" } } } - """, google_extensions_pb2.EventLabel()) + """, ml_extensions_pb2.EventLabel()) # pylint: enable=line-too-long (filtered_count, got_list) = bundle_to_seqex_util.get_trigger_labels_pair( diff --git a/spec/google/BUILD b/spec/google/BUILD index 1c64bb329..3c85f3dc6 100644 --- a/spec/google/BUILD +++ b/spec/google/BUILD @@ -9,7 +9,7 @@ package(default_visibility = ["//visibility:public"]) gen_fhir_definitions_and_protos( name = "stu3", extensions = [ - "google_extensions.prototxt", + "fhirproto_extensions.prototxt", ], package_info = "google_stu3_package_info.prototxt", separate_extensions = True, @@ -18,7 +18,7 @@ gen_fhir_definitions_and_protos( gen_fhir_definitions_and_protos( name = "r4", extensions = [ - "google_extensions.prototxt", + "fhirproto_extensions.prototxt", ], package_info = "google_r4_package_info.prototxt", separate_extensions = True, diff --git a/spec/google/google_extensions.prototxt b/spec/google/fhirproto_extensions.prototxt similarity index 100% rename from spec/google/google_extensions.prototxt rename to spec/google/fhirproto_extensions.prototxt