diff --git a/python/ga4gh/schemas/_protocol_version.py b/python/ga4gh/schemas/_protocol_version.py index 20103a4e..e327d80e 100644 --- a/python/ga4gh/schemas/_protocol_version.py +++ b/python/ga4gh/schemas/_protocol_version.py @@ -1,2 +1,2 @@ # File generated by scripts/process_schemas.py; do not edit -version = '0.6.0a10' +version = '0.6.0a9' diff --git a/python/ga4gh/schemas/ga4gh/rna_quantification_pb2.py b/python/ga4gh/schemas/ga4gh/rna_quantification_pb2.py index 7dab68bb..e34b77f6 100644 --- a/python/ga4gh/schemas/ga4gh/rna_quantification_pb2.py +++ b/python/ga4gh/schemas/ga4gh/rna_quantification_pb2.py @@ -21,7 +21,7 @@ name='ga4gh/schemas/ga4gh/rna_quantification.proto', package='ga4gh.schemas.ga4gh', syntax='proto3', - serialized_pb=_b('\n,ga4gh/schemas/ga4gh/rna_quantification.proto\x12\x13ga4gh.schemas.ga4gh\x1a ga4gh/schemas/ga4gh/common.proto\"y\n\x14RnaQuantificationSet\x12\n\n\x02id\x18\x01 \x01(\t\x12\x12\n\ndataset_id\x18\x02 \x01(\t\x12\x0c\n\x04name\x18\x03 \x01(\t\x12\x33\n\nattributes\x18\x04 \x01(\x0b\x32\x1f.ga4gh.schemas.ga4gh.Attributes\"\x91\x02\n\x11RnaQuantification\x12\n\n\x02id\x18\x01 \x01(\t\x12\x0c\n\x04name\x18\x02 \x01(\t\x12\x14\n\x0c\x62iosample_id\x18\x08 \x01(\t\x12\x13\n\x0b\x64\x65scription\x18\x03 \x01(\t\x12\x16\n\x0eread_group_ids\x18\x04 \x03(\t\x12.\n\x08programs\x18\x05 \x03(\x0b\x32\x1c.ga4gh.schemas.ga4gh.Program\x12\x17\n\x0f\x66\x65\x61ture_set_ids\x18\x06 \x03(\t\x12!\n\x19rna_quantification_set_id\x18\x07 \x01(\t\x12\x33\n\nattributes\x18\t \x01(\x0b\x32\x1f.ga4gh.schemas.ga4gh.Attributes\"\xd0\x02\n\x0f\x45xpressionLevel\x12\n\n\x02id\x18\x01 \x01(\t\x12\x0c\n\x04name\x18\x02 \x01(\t\x12\x12\n\nfeature_id\x18\x03 \x01(\t\x12\x1d\n\x15rna_quantification_id\x18\x04 \x01(\t\x12\x16\n\x0eraw_read_count\x18\x05 \x01(\x02\x12\x12\n\nexpression\x18\x06 \x01(\x02\x12\x15\n\ris_normalized\x18\x07 \x01(\x08\x12\x32\n\x05units\x18\x08 \x01(\x0e\x32#.ga4gh.schemas.ga4gh.ExpressionUnit\x12\r\n\x05score\x18\t \x01(\x02\x12\x19\n\x11\x63onf_interval_low\x18\n \x01(\x02\x12\x1a\n\x12\x63onf_interval_high\x18\x0b \x01(\x02\x12\x33\n\nattributes\x18\x0c \x01(\x0b\x32\x1f.ga4gh.schemas.ga4gh.Attributes*D\n\x0e\x45xpressionUnit\x12\x1f\n\x1b\x45XPRESSION_UNIT_UNSPECIFIED\x10\x00\x12\x08\n\x04\x46PKM\x10\x01\x12\x07\n\x03TPM\x10\x02\x62\x06proto3') + serialized_pb=_b('\n,ga4gh/schemas/ga4gh/rna_quantification.proto\x12\x13ga4gh.schemas.ga4gh\x1a ga4gh/schemas/ga4gh/common.proto\"y\n\x14RnaQuantificationSet\x12\n\n\x02id\x18\x01 \x01(\t\x12\x12\n\ndataset_id\x18\x02 \x01(\t\x12\x0c\n\x04name\x18\x03 \x01(\t\x12\x33\n\nattributes\x18\x04 \x01(\x0b\x32\x1f.ga4gh.schemas.ga4gh.Attributes\"\x91\x02\n\x11RnaQuantification\x12\n\n\x02id\x18\x01 \x01(\t\x12\x0c\n\x04name\x18\x02 \x01(\t\x12\x14\n\x0c\x62iosample_id\x18\x08 \x01(\t\x12\x13\n\x0b\x64\x65scription\x18\x03 \x01(\t\x12\x16\n\x0eread_group_ids\x18\x04 \x03(\t\x12.\n\x08programs\x18\x05 \x03(\x0b\x32\x1c.ga4gh.schemas.ga4gh.Program\x12\x17\n\x0f\x66\x65\x61ture_set_ids\x18\x06 \x03(\t\x12!\n\x19rna_quantification_set_id\x18\x07 \x01(\t\x12\x33\n\nattributes\x18\t \x01(\x0b\x32\x1f.ga4gh.schemas.ga4gh.Attributes\"\xbc\x02\n\x0f\x45xpressionLevel\x12\n\n\x02id\x18\x01 \x01(\t\x12\x0c\n\x04name\x18\x02 \x01(\t\x12\x1d\n\x15rna_quantification_id\x18\x04 \x01(\t\x12\x16\n\x0eraw_read_count\x18\x05 \x01(\x02\x12\x12\n\nexpression\x18\x06 \x01(\x02\x12\x15\n\ris_normalized\x18\x07 \x01(\x08\x12\x32\n\x05units\x18\x08 \x01(\x0e\x32#.ga4gh.schemas.ga4gh.ExpressionUnit\x12\r\n\x05score\x18\t \x01(\x02\x12\x19\n\x11\x63onf_interval_low\x18\n \x01(\x02\x12\x1a\n\x12\x63onf_interval_high\x18\x0b \x01(\x02\x12\x33\n\nattributes\x18\x0c \x01(\x0b\x32\x1f.ga4gh.schemas.ga4gh.Attributes*D\n\x0e\x45xpressionUnit\x12\x1f\n\x1b\x45XPRESSION_UNIT_UNSPECIFIED\x10\x00\x12\x08\n\x04\x46PKM\x10\x01\x12\x07\n\x03TPM\x10\x02\x62\x06proto3') , dependencies=[ga4gh_dot_schemas_dot_ga4gh_dot_common__pb2.DESCRIPTOR,]) _sym_db.RegisterFileDescriptor(DESCRIPTOR) @@ -47,8 +47,8 @@ ], containing_type=None, options=None, - serialized_start=841, - serialized_end=909, + serialized_start=821, + serialized_end=889, ) _sym_db.RegisterEnumDescriptor(_EXPRESSIONUNIT) @@ -220,70 +220,63 @@ is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='feature_id', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.feature_id', index=2, - number=3, type=9, cpp_type=9, label=1, - has_default_value=False, default_value=_b("").decode('utf-8'), - message_type=None, enum_type=None, containing_type=None, - is_extension=False, extension_scope=None, - options=None), - _descriptor.FieldDescriptor( - name='rna_quantification_id', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.rna_quantification_id', index=3, + name='rna_quantification_id', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.rna_quantification_id', index=2, number=4, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='raw_read_count', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.raw_read_count', index=4, + name='raw_read_count', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.raw_read_count', index=3, number=5, type=2, cpp_type=6, label=1, has_default_value=False, default_value=float(0), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='expression', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.expression', index=5, + name='expression', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.expression', index=4, number=6, type=2, cpp_type=6, label=1, has_default_value=False, default_value=float(0), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='is_normalized', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.is_normalized', index=6, + name='is_normalized', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.is_normalized', index=5, number=7, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='units', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.units', index=7, + name='units', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.units', index=6, number=8, type=14, cpp_type=8, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='score', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.score', index=8, + name='score', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.score', index=7, number=9, type=2, cpp_type=6, label=1, has_default_value=False, default_value=float(0), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='conf_interval_low', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.conf_interval_low', index=9, + name='conf_interval_low', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.conf_interval_low', index=8, number=10, type=2, cpp_type=6, label=1, has_default_value=False, default_value=float(0), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='conf_interval_high', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.conf_interval_high', index=10, + name='conf_interval_high', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.conf_interval_high', index=9, number=11, type=2, cpp_type=6, label=1, has_default_value=False, default_value=float(0), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='attributes', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.attributes', index=11, + name='attributes', full_name='ga4gh.schemas.ga4gh.ExpressionLevel.attributes', index=10, number=12, type=11, cpp_type=10, label=1, has_default_value=False, default_value=None, message_type=None, enum_type=None, containing_type=None, @@ -302,7 +295,7 @@ oneofs=[ ], serialized_start=503, - serialized_end=839, + serialized_end=819, ) _RNAQUANTIFICATIONSET.fields_by_name['attributes'].message_type = ga4gh_dot_schemas_dot_ga4gh_dot_common__pb2._ATTRIBUTES diff --git a/python/ga4gh/schemas/ga4gh/rna_quantification_service_pb2.py b/python/ga4gh/schemas/ga4gh/rna_quantification_service_pb2.py index 62d445ca..02b65bf7 100644 --- a/python/ga4gh/schemas/ga4gh/rna_quantification_service_pb2.py +++ b/python/ga4gh/schemas/ga4gh/rna_quantification_service_pb2.py @@ -21,7 +21,7 @@ name='ga4gh/schemas/ga4gh/rna_quantification_service.proto', package='ga4gh.schemas.ga4gh', syntax='proto3', - serialized_pb=_b('\n4ga4gh/schemas/ga4gh/rna_quantification_service.proto\x12\x13ga4gh.schemas.ga4gh\x1a,ga4gh/schemas/ga4gh/rna_quantification.proto\x1a*ga4gh/schemas/google/api/annotations.proto\"_\n\"SearchRnaQuantificationSetsRequest\x12\x12\n\ndataset_id\x18\x01 \x01(\t\x12\x11\n\tpage_size\x18\x02 \x01(\x05\x12\x12\n\npage_token\x18\x03 \x01(\t\"\x8a\x01\n#SearchRnaQuantificationSetsResponse\x12J\n\x17rna_quantification_sets\x18\x01 \x03(\x0b\x32).ga4gh.schemas.ga4gh.RnaQuantificationSet\x12\x17\n\x0fnext_page_token\x18\x02 \x01(\t\"C\n\x1eGetRnaQuantificationSetRequest\x12!\n\x19rna_quantification_set_id\x18\x01 \x01(\t\"\x81\x01\n\x1fSearchRnaQuantificationsRequest\x12!\n\x19rna_quantification_set_id\x18\x01 \x01(\t\x12\x14\n\x0c\x62iosample_id\x18\x04 \x01(\t\x12\x11\n\tpage_size\x18\x02 \x01(\x05\x12\x12\n\npage_token\x18\x03 \x01(\t\"\x80\x01\n SearchRnaQuantificationsResponse\x12\x43\n\x13rna_quantifications\x18\x01 \x03(\x0b\x32&.ga4gh.schemas.ga4gh.RnaQuantification\x12\x17\n\x0fnext_page_token\x18\x02 \x01(\t\"<\n\x1bGetRnaQuantificationRequest\x12\x1d\n\x15rna_quantification_id\x18\x01 \x01(\t\"\x8d\x01\n\x1dSearchExpressionLevelsRequest\x12\x1d\n\x15rna_quantification_id\x18\x01 \x01(\t\x12\x13\n\x0b\x66\x65\x61ture_ids\x18\x02 \x03(\t\x12\x11\n\tthreshold\x18\x03 \x01(\x02\x12\x11\n\tpage_size\x18\x04 \x01(\x05\x12\x12\n\npage_token\x18\x05 \x01(\t\"z\n\x1eSearchExpressionLevelsResponse\x12?\n\x11\x65xpression_levels\x18\x01 \x03(\x0b\x32$.ga4gh.schemas.ga4gh.ExpressionLevel\x12\x17\n\x0fnext_page_token\x18\x02 \x01(\t\"8\n\x19GetExpressionLevelRequest\x12\x1b\n\x13\x65xpression_level_id\x18\x01 \x01(\t2\xe5\x08\n\x18RnaQuantificationService\x12\xc3\x01\n\x1bSearchRnaQuantificationSets\x12\x37.ga4gh.schemas.ga4gh.SearchRnaQuantificationSetsRequest\x1a\x38.ga4gh.schemas.ga4gh.SearchRnaQuantificationSetsResponse\"1\x82\xd3\xe4\x93\x02+\"&/v0.6.0a9/rnaquantificationsets/search:\x01*\x12\xbe\x01\n\x17GetRnaQuantificationSet\x12\x33.ga4gh.schemas.ga4gh.GetRnaQuantificationSetRequest\x1a).ga4gh.schemas.ga4gh.RnaQuantificationSet\"C\x82\xd3\xe4\x93\x02=\x12;/v0.6.0a9/rnaquantificationsets/{rna_quantification_set_id}\x12\xb7\x01\n\x18SearchRnaQuantifications\x12\x34.ga4gh.schemas.ga4gh.SearchRnaQuantificationsRequest\x1a\x35.ga4gh.schemas.ga4gh.SearchRnaQuantificationsResponse\".\x82\xd3\xe4\x93\x02(\"#/v0.6.0a9/rnaquantifications/search:\x01*\x12\xae\x01\n\x14GetRnaQuantification\x12\x30.ga4gh.schemas.ga4gh.GetRnaQuantificationRequest\x1a&.ga4gh.schemas.ga4gh.RnaQuantification\"<\x82\xd3\xe4\x93\x02\x36\x12\x34/v0.6.0a9/rnaquantifications/{rna_quantification_id}\x12\xaf\x01\n\x16SearchExpressionLevels\x12\x32.ga4gh.schemas.ga4gh.SearchExpressionLevelsRequest\x1a\x33.ga4gh.schemas.ga4gh.SearchExpressionLevelsResponse\",\x82\xd3\xe4\x93\x02&\"!/v0.6.0a9/expressionlevels/search:\x01*\x12\xa4\x01\n\x12GetExpressionLevel\x12..ga4gh.schemas.ga4gh.GetExpressionLevelRequest\x1a$.ga4gh.schemas.ga4gh.ExpressionLevel\"8\x82\xd3\xe4\x93\x02\x32\x12\x30/v0.6.0a9/expressionlevels/{expression_level_id}b\x06proto3') + serialized_pb=_b('\n4ga4gh/schemas/ga4gh/rna_quantification_service.proto\x12\x13ga4gh.schemas.ga4gh\x1a,ga4gh/schemas/ga4gh/rna_quantification.proto\x1a*ga4gh/schemas/google/api/annotations.proto\"_\n\"SearchRnaQuantificationSetsRequest\x12\x12\n\ndataset_id\x18\x01 \x01(\t\x12\x11\n\tpage_size\x18\x02 \x01(\x05\x12\x12\n\npage_token\x18\x03 \x01(\t\"\x8a\x01\n#SearchRnaQuantificationSetsResponse\x12J\n\x17rna_quantification_sets\x18\x01 \x03(\x0b\x32).ga4gh.schemas.ga4gh.RnaQuantificationSet\x12\x17\n\x0fnext_page_token\x18\x02 \x01(\t\"C\n\x1eGetRnaQuantificationSetRequest\x12!\n\x19rna_quantification_set_id\x18\x01 \x01(\t\"\x81\x01\n\x1fSearchRnaQuantificationsRequest\x12!\n\x19rna_quantification_set_id\x18\x01 \x01(\t\x12\x14\n\x0c\x62iosample_id\x18\x04 \x01(\t\x12\x11\n\tpage_size\x18\x02 \x01(\x05\x12\x12\n\npage_token\x18\x03 \x01(\t\"\x80\x01\n SearchRnaQuantificationsResponse\x12\x43\n\x13rna_quantifications\x18\x01 \x03(\x0b\x32&.ga4gh.schemas.ga4gh.RnaQuantification\x12\x17\n\x0fnext_page_token\x18\x02 \x01(\t\"<\n\x1bGetRnaQuantificationRequest\x12\x1d\n\x15rna_quantification_id\x18\x01 \x01(\t\"\x87\x01\n\x1dSearchExpressionLevelsRequest\x12\x1d\n\x15rna_quantification_id\x18\x01 \x01(\t\x12\r\n\x05names\x18\x06 \x03(\t\x12\x11\n\tthreshold\x18\x03 \x01(\x02\x12\x11\n\tpage_size\x18\x04 \x01(\x05\x12\x12\n\npage_token\x18\x05 \x01(\t\"z\n\x1eSearchExpressionLevelsResponse\x12?\n\x11\x65xpression_levels\x18\x01 \x03(\x0b\x32$.ga4gh.schemas.ga4gh.ExpressionLevel\x12\x17\n\x0fnext_page_token\x18\x02 \x01(\t\"8\n\x19GetExpressionLevelRequest\x12\x1b\n\x13\x65xpression_level_id\x18\x01 \x01(\t2\xe5\x08\n\x18RnaQuantificationService\x12\xc3\x01\n\x1bSearchRnaQuantificationSets\x12\x37.ga4gh.schemas.ga4gh.SearchRnaQuantificationSetsRequest\x1a\x38.ga4gh.schemas.ga4gh.SearchRnaQuantificationSetsResponse\"1\x82\xd3\xe4\x93\x02+\"&/v0.6.0a9/rnaquantificationsets/search:\x01*\x12\xbe\x01\n\x17GetRnaQuantificationSet\x12\x33.ga4gh.schemas.ga4gh.GetRnaQuantificationSetRequest\x1a).ga4gh.schemas.ga4gh.RnaQuantificationSet\"C\x82\xd3\xe4\x93\x02=\x12;/v0.6.0a9/rnaquantificationsets/{rna_quantification_set_id}\x12\xb7\x01\n\x18SearchRnaQuantifications\x12\x34.ga4gh.schemas.ga4gh.SearchRnaQuantificationsRequest\x1a\x35.ga4gh.schemas.ga4gh.SearchRnaQuantificationsResponse\".\x82\xd3\xe4\x93\x02(\"#/v0.6.0a9/rnaquantifications/search:\x01*\x12\xae\x01\n\x14GetRnaQuantification\x12\x30.ga4gh.schemas.ga4gh.GetRnaQuantificationRequest\x1a&.ga4gh.schemas.ga4gh.RnaQuantification\"<\x82\xd3\xe4\x93\x02\x36\x12\x34/v0.6.0a9/rnaquantifications/{rna_quantification_id}\x12\xaf\x01\n\x16SearchExpressionLevels\x12\x32.ga4gh.schemas.ga4gh.SearchExpressionLevelsRequest\x1a\x33.ga4gh.schemas.ga4gh.SearchExpressionLevelsResponse\",\x82\xd3\xe4\x93\x02&\"!/v0.6.0a9/expressionlevels/search:\x01*\x12\xa4\x01\n\x12GetExpressionLevel\x12..ga4gh.schemas.ga4gh.GetExpressionLevelRequest\x1a$.ga4gh.schemas.ga4gh.ExpressionLevel\"8\x82\xd3\xe4\x93\x02\x32\x12\x30/v0.6.0a9/expressionlevels/{expression_level_id}b\x06proto3') , dependencies=[ga4gh_dot_schemas_dot_ga4gh_dot_rna__quantification__pb2.DESCRIPTOR,ga4gh_dot_schemas_dot_google_dot_api_dot_annotations__pb2.DESCRIPTOR,]) _sym_db.RegisterFileDescriptor(DESCRIPTOR) @@ -279,8 +279,8 @@ is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( - name='feature_ids', full_name='ga4gh.schemas.ga4gh.SearchExpressionLevelsRequest.feature_ids', index=1, - number=2, type=9, cpp_type=9, label=3, + name='names', full_name='ga4gh.schemas.ga4gh.SearchExpressionLevelsRequest.names', index=1, + number=6, type=9, cpp_type=9, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, @@ -319,7 +319,7 @@ oneofs=[ ], serialized_start=800, - serialized_end=941, + serialized_end=935, ) @@ -356,8 +356,8 @@ extension_ranges=[], oneofs=[ ], - serialized_start=943, - serialized_end=1065, + serialized_start=937, + serialized_end=1059, ) @@ -387,8 +387,8 @@ extension_ranges=[], oneofs=[ ], - serialized_start=1067, - serialized_end=1123, + serialized_start=1061, + serialized_end=1117, ) _SEARCHRNAQUANTIFICATIONSETSRESPONSE.fields_by_name['rna_quantification_sets'].message_type = ga4gh_dot_schemas_dot_ga4gh_dot_rna__quantification__pb2._RNAQUANTIFICATIONSET diff --git a/src/main/proto/ga4gh/rna_quantification.proto b/src/main/proto/ga4gh/rna_quantification.proto index 24b7ac0f..25fda6ca 100644 --- a/src/main/proto/ga4gh/rna_quantification.proto +++ b/src/main/proto/ga4gh/rna_quantification.proto @@ -80,9 +80,6 @@ message ExpressionLevel { // Name string name = 2; - // Id of the feature - string feature_id = 3; - // The associated RnaQuantification string rna_quantification_id = 4; diff --git a/src/main/proto/ga4gh/rna_quantification_service.proto b/src/main/proto/ga4gh/rna_quantification_service.proto index e6573a0e..8bbd376d 100644 --- a/src/main/proto/ga4gh/rna_quantification_service.proto +++ b/src/main/proto/ga4gh/rna_quantification_service.proto @@ -158,10 +158,10 @@ message GetRnaQuantificationRequest { message SearchExpressionLevelsRequest { // The rnaQuantification to restrict search to. string rna_quantification_id = 1; - - // Only return expressions with any of the specified feature_ids. - repeated string feature_ids = 2; + // Only return expressions with any of the names (strict string matching). + repeated string names = 6; + // Only return ExpressionLevel records with expressions exceeding // this value. (Defaults to 0.0) float threshold = 3;