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A Protobuf schema for capturing clinical phenotypes
# -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: base.proto
import sys
_b=sys.version_info[0]<3 and (lambda x:x) or (lambda x:x.encode('latin1'))
from google.protobuf.internal import enum_type_wrapper
from google.protobuf import descriptor as _descriptor
from google.protobuf import message as _message
from google.protobuf import reflection as _reflection
from google.protobuf import symbol_database as _symbol_database
# @@protoc_insertion_point(imports)
_sym_db = _symbol_database.Default()
from google.protobuf import timestamp_pb2 as google_dot_protobuf_dot_timestamp__pb2
from validate import validate_pb2 as validate_dot_validate__pb2
DESCRIPTOR = _descriptor.FileDescriptor(
name='base.proto',
package='org.phenopackets.schema.v1.core',
syntax='proto3',
serialized_options=_b('\n\037org.phenopackets.schema.v1.coreP\001'),
serialized_pb=_b('\n\nbase.proto\x12\x1forg.phenopackets.schema.v1.core\x1a\x1fgoogle/protobuf/timestamp.proto\x1a\x17validate/validate.proto\"\xce\x02\n\x08MetaData\x12+\n\x07\x63reated\x18\x01 \x01(\x0b\x32\x1a.google.protobuf.Timestamp\x12\x12\n\ncreated_by\x18\x02 \x01(\t\x12\x14\n\x0csubmitted_by\x18\x03 \x01(\t\x12<\n\tresources\x18\x04 \x03(\x0b\x32).org.phenopackets.schema.v1.core.Resource\x12\x38\n\x07updates\x18\x05 \x03(\x0b\x32\'.org.phenopackets.schema.v1.core.Update\x12\"\n\x1aphenopacket_schema_version\x18\x06 \x01(\t\x12O\n\x13\x65xternal_references\x18\x07 \x03(\x0b\x32\x32.org.phenopackets.schema.v1.core.ExternalReference\"f\n\x06Update\x12\x37\n\ttimestamp\x18\x01 \x01(\x0b\x32\x1a.google.protobuf.TimestampB\x08\xfa\x42\x05\xb2\x01\x02\x08\x01\x12\x12\n\nupdated_by\x18\x02 \x01(\t\x12\x0f\n\x07\x63omment\x18\x03 \x01(\t\"p\n\x08Resource\x12\n\n\x02id\x18\x01 \x01(\t\x12\x0c\n\x04name\x18\x02 \x01(\t\x12\x0b\n\x03url\x18\x03 \x01(\t\x12\x0f\n\x07version\x18\x04 \x01(\t\x12\x18\n\x10namespace_prefix\x18\x05 \x01(\t\x12\x12\n\niri_prefix\x18\x06 \x01(\t\"*\n\rOntologyClass\x12\n\n\x02id\x18\x01 \x01(\t\x12\r\n\x05label\x18\x02 \x01(\t\"\x93\x04\n\x11PhenotypicFeature\x12\x13\n\x0b\x64\x65scription\x18\x01 \x01(\t\x12<\n\x04type\x18\x02 \x01(\x0b\x32..org.phenopackets.schema.v1.core.OntologyClass\x12\x0f\n\x07negated\x18\x03 \x01(\x08\x12@\n\x08severity\x18\x04 \x01(\x0b\x32..org.phenopackets.schema.v1.core.OntologyClass\x12\x41\n\tmodifiers\x18\x05 \x03(\x0b\x32..org.phenopackets.schema.v1.core.OntologyClass\x12<\n\x0c\x61ge_of_onset\x18\x06 \x01(\x0b\x32$.org.phenopackets.schema.v1.core.AgeH\x00\x12G\n\x12\x61ge_range_of_onset\x18\x07 \x01(\x0b\x32).org.phenopackets.schema.v1.core.AgeRangeH\x00\x12H\n\x0e\x63lass_of_onset\x18\t \x01(\x0b\x32..org.phenopackets.schema.v1.core.OntologyClassH\x00\x12;\n\x08\x65vidence\x18\n \x03(\x0b\x32).org.phenopackets.schema.v1.core.EvidenceB\x07\n\x05onset\"\x98\x01\n\x08\x45vidence\x12\x45\n\revidence_code\x18\x01 \x01(\x0b\x32..org.phenopackets.schema.v1.core.OntologyClass\x12\x45\n\treference\x18\x02 \x01(\x0b\x32\x32.org.phenopackets.schema.v1.core.ExternalReference\"4\n\x11\x45xternalReference\x12\n\n\x02id\x18\x01 \x01(\t\x12\x13\n\x0b\x64\x65scription\x18\x02 \x01(\t\"\xb7\x03\n\nIndividual\x12\n\n\x02id\x18\x01 \x01(\t\x12\x15\n\ralternate_ids\x18\x02 \x03(\t\x12\x31\n\rdate_of_birth\x18\x03 \x01(\x0b\x32\x1a.google.protobuf.Timestamp\x12\x41\n\x11\x61ge_at_collection\x18\x04 \x01(\x0b\x32$.org.phenopackets.schema.v1.core.AgeH\x00\x12L\n\x17\x61ge_range_at_collection\x18\x05 \x01(\x0b\x32).org.phenopackets.schema.v1.core.AgeRangeH\x00\x12\x31\n\x03sex\x18\x06 \x01(\x0e\x32$.org.phenopackets.schema.v1.core.Sex\x12\x46\n\x0ekaryotypic_sex\x18\x07 \x01(\x0e\x32..org.phenopackets.schema.v1.core.KaryotypicSex\x12@\n\x08taxonomy\x18\x08 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\x01(\t\x12\x15\n\ralternate_ids\x18\x02 \x03(\t\x12\x0e\n\x06symbol\x18\x03 \x01(\t\"\xe3\x02\n\x07Variant\x12\x42\n\x0bhgvs_allele\x18\x02 \x01(\x0b\x32+.org.phenopackets.schema.v1.core.HgvsAlleleH\x00\x12@\n\nvcf_allele\x18\x03 \x01(\x0b\x32*.org.phenopackets.schema.v1.core.VcfAlleleH\x00\x12\x42\n\x0bspdi_allele\x18\x04 \x01(\x0b\x32+.org.phenopackets.schema.v1.core.SpdiAlleleH\x00\x12\x42\n\x0biscn_allele\x18\x05 \x01(\x0b\x32+.org.phenopackets.schema.v1.core.IscnAlleleH\x00\x12@\n\x08zygosity\x18\x06 \x01(\x0b\x32..org.phenopackets.schema.v1.core.OntologyClassB\x08\n\x06\x61llele\"&\n\nHgvsAllele\x12\n\n\x02id\x18\x01 \x01(\t\x12\x0c\n\x04hgvs\x18\x02 \x01(\t\"\x87\x01\n\tVcfAllele\x12\x13\n\x0bvcf_version\x18\x01 \x01(\t\x12\x17\n\x0fgenome_assembly\x18\x02 \x01(\t\x12\n\n\x02id\x18\x03 \x01(\t\x12\x0b\n\x03\x63hr\x18\x04 \x01(\t\x12\x0b\n\x03pos\x18\x05 \x01(\x05\x12\x0b\n\x03ref\x18\x06 \x01(\t\x12\x0b\n\x03\x61lt\x18\x07 \x01(\t\x12\x0c\n\x04info\x18\x08 \x01(\t\"o\n\nSpdiAllele\x12\n\n\x02id\x18\x01 \x01(\t\x12\x0e\n\x06seq_id\x18\x02 \x01(\t\x12\x10\n\x08position\x18\x03 \x01(\x05\x12\x18\n\x10\x64\x65leted_sequence\x18\x04 \x01(\t\x12\x19\n\x11inserted_sequence\x18\x05 \x01(\t\"&\n\nIscnAllele\x12\n\n\x02id\x18\x01 \x01(\t\x12\x0c\n\x04iscn\x18\x02 \x01(\t*;\n\x03Sex\x12\x0f\n\x0bUNKNOWN_SEX\x10\x00\x12\n\n\x06\x46\x45MALE\x10\x01\x12\x08\n\x04MALE\x10\x02\x12\r\n\tOTHER_SEX\x10\x03*\x8c\x01\n\rKaryotypicSex\x12\x15\n\x11UNKNOWN_KARYOTYPE\x10\x00\x12\x06\n\x02XX\x10\x01\x12\x06\n\x02XY\x10\x02\x12\x06\n\x02XO\x10\x03\x12\x07\n\x03XXY\x10\x04\x12\x07\n\x03XXX\x10\x05\x12\x08\n\x04XXYY\x10\x06\x12\x08\n\x04XXXY\x10\x07\x12\x08\n\x04XXXX\x10\x08\x12\x07\n\x03XYY\x10\t\x12\x13\n\x0fOTHER_KARYOTYPE\x10\nB#\n\x1forg.phenopackets.schema.v1.coreP\x01\x62\x06proto3')
,
dependencies=[google_dot_protobuf_dot_timestamp__pb2.DESCRIPTOR,validate_dot_validate__pb2.DESCRIPTOR,])
_SEX = _descriptor.EnumDescriptor(
name='Sex',
full_name='org.phenopackets.schema.v1.core.Sex',
filename=None,
file=DESCRIPTOR,
values=[
_descriptor.EnumValueDescriptor(
name='UNKNOWN_SEX', index=0, number=0,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='FEMALE', index=1, number=1,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='MALE', index=2, number=2,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='OTHER_SEX', index=3, number=3,
serialized_options=None,
type=None),
],
containing_type=None,
serialized_options=None,
serialized_start=5073,
serialized_end=5132,
)
_sym_db.RegisterEnumDescriptor(_SEX)
Sex = enum_type_wrapper.EnumTypeWrapper(_SEX)
_KARYOTYPICSEX = _descriptor.EnumDescriptor(
name='KaryotypicSex',
full_name='org.phenopackets.schema.v1.core.KaryotypicSex',
filename=None,
file=DESCRIPTOR,
values=[
_descriptor.EnumValueDescriptor(
name='UNKNOWN_KARYOTYPE', index=0, number=0,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XX', index=1, number=1,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XY', index=2, number=2,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XO', index=3, number=3,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XXY', index=4, number=4,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XXX', index=5, number=5,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XXYY', index=6, number=6,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XXXY', index=7, number=7,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XXXX', index=8, number=8,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='XYY', index=9, number=9,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='OTHER_KARYOTYPE', index=10, number=10,
serialized_options=None,
type=None),
],
containing_type=None,
serialized_options=None,
serialized_start=5135,
serialized_end=5275,
)
_sym_db.RegisterEnumDescriptor(_KARYOTYPICSEX)
KaryotypicSex = enum_type_wrapper.EnumTypeWrapper(_KARYOTYPICSEX)
UNKNOWN_SEX = 0
FEMALE = 1
MALE = 2
OTHER_SEX = 3
UNKNOWN_KARYOTYPE = 0
XX = 1
XY = 2
XO = 3
XXY = 4
XXX = 5
XXYY = 6
XXXY = 7
XXXX = 8
XYY = 9
OTHER_KARYOTYPE = 10
_PEDIGREE_PERSON_AFFECTEDSTATUS = _descriptor.EnumDescriptor(
name='AffectedStatus',
full_name='org.phenopackets.schema.v1.core.Pedigree.Person.AffectedStatus',
filename=None,
file=DESCRIPTOR,
values=[
_descriptor.EnumValueDescriptor(
name='MISSING', index=0, number=0,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='UNAFFECTED', index=1, number=1,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='AFFECTED', index=2, number=2,
serialized_options=None,
type=None),
],
containing_type=None,
serialized_options=None,
serialized_start=3850,
serialized_end=3909,
)
_sym_db.RegisterEnumDescriptor(_PEDIGREE_PERSON_AFFECTEDSTATUS)
_HTSFILE_HTSFORMAT = _descriptor.EnumDescriptor(
name='HtsFormat',
full_name='org.phenopackets.schema.v1.core.HtsFile.HtsFormat',
filename=None,
file=DESCRIPTOR,
values=[
_descriptor.EnumValueDescriptor(
name='UNKNOWN', index=0, number=0,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='SAM', index=1, number=1,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='BAM', index=2, number=2,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='CRAM', index=3, number=3,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='VCF', index=4, number=4,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='BCF', index=5, number=5,
serialized_options=None,
type=None),
_descriptor.EnumValueDescriptor(
name='GVCF', index=6, number=6,
serialized_options=None,
type=None),
],
containing_type=None,
serialized_options=None,
serialized_start=4243,
serialized_end=4323,
)
_sym_db.RegisterEnumDescriptor(_HTSFILE_HTSFORMAT)
_METADATA = _descriptor.Descriptor(
name='MetaData',
full_name='org.phenopackets.schema.v1.core.MetaData',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='created', full_name='org.phenopackets.schema.v1.core.MetaData.created', index=0,
number=1, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='created_by', full_name='org.phenopackets.schema.v1.core.MetaData.created_by', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='submitted_by', full_name='org.phenopackets.schema.v1.core.MetaData.submitted_by', 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='resources', full_name='org.phenopackets.schema.v1.core.MetaData.resources', index=3,
number=4, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='updates', full_name='org.phenopackets.schema.v1.core.MetaData.updates', index=4,
number=5, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='phenopacket_schema_version', full_name='org.phenopackets.schema.v1.core.MetaData.phenopacket_schema_version', index=5,
number=6, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='external_references', full_name='org.phenopackets.schema.v1.core.MetaData.external_references', index=6,
number=7, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=106,
serialized_end=440,
)
_UPDATE = _descriptor.Descriptor(
name='Update',
full_name='org.phenopackets.schema.v1.core.Update',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='timestamp', full_name='org.phenopackets.schema.v1.core.Update.timestamp', index=0,
number=1, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=_b('\372B\005\262\001\002\010\001'), file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='updated_by', full_name='org.phenopackets.schema.v1.core.Update.updated_by', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='comment', full_name='org.phenopackets.schema.v1.core.Update.comment', 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=442,
serialized_end=544,
)
_RESOURCE = _descriptor.Descriptor(
name='Resource',
full_name='org.phenopackets.schema.v1.core.Resource',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.Resource.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='name', full_name='org.phenopackets.schema.v1.core.Resource.name', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='url', full_name='org.phenopackets.schema.v1.core.Resource.url', 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='version', full_name='org.phenopackets.schema.v1.core.Resource.version', index=3,
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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='namespace_prefix', full_name='org.phenopackets.schema.v1.core.Resource.namespace_prefix', index=4,
number=5, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='iri_prefix', full_name='org.phenopackets.schema.v1.core.Resource.iri_prefix', index=5,
number=6, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=546,
serialized_end=658,
)
_ONTOLOGYCLASS = _descriptor.Descriptor(
name='OntologyClass',
full_name='org.phenopackets.schema.v1.core.OntologyClass',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.OntologyClass.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='label', full_name='org.phenopackets.schema.v1.core.OntologyClass.label', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=660,
serialized_end=702,
)
_PHENOTYPICFEATURE = _descriptor.Descriptor(
name='PhenotypicFeature',
full_name='org.phenopackets.schema.v1.core.PhenotypicFeature',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='description', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.description', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='type', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.type', index=1,
number=2, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='negated', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.negated', index=2,
number=3, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='severity', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.severity', index=3,
number=4, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='modifiers', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.modifiers', index=4,
number=5, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='age_of_onset', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.age_of_onset', index=5,
number=6, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='age_range_of_onset', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.age_range_of_onset', index=6,
number=7, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='class_of_onset', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.class_of_onset', index=7,
number=9, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='evidence', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.evidence', index=8,
number=10, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
_descriptor.OneofDescriptor(
name='onset', full_name='org.phenopackets.schema.v1.core.PhenotypicFeature.onset',
index=0, containing_type=None, fields=[]),
],
serialized_start=705,
serialized_end=1236,
)
_EVIDENCE = _descriptor.Descriptor(
name='Evidence',
full_name='org.phenopackets.schema.v1.core.Evidence',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='evidence_code', full_name='org.phenopackets.schema.v1.core.Evidence.evidence_code', index=0,
number=1, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='reference', full_name='org.phenopackets.schema.v1.core.Evidence.reference', index=1,
number=2, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=1239,
serialized_end=1391,
)
_EXTERNALREFERENCE = _descriptor.Descriptor(
name='ExternalReference',
full_name='org.phenopackets.schema.v1.core.ExternalReference',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.ExternalReference.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='description', full_name='org.phenopackets.schema.v1.core.ExternalReference.description', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=1393,
serialized_end=1445,
)
_INDIVIDUAL = _descriptor.Descriptor(
name='Individual',
full_name='org.phenopackets.schema.v1.core.Individual',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.Individual.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='alternate_ids', full_name='org.phenopackets.schema.v1.core.Individual.alternate_ids', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='date_of_birth', full_name='org.phenopackets.schema.v1.core.Individual.date_of_birth', index=2,
number=3, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='age_at_collection', full_name='org.phenopackets.schema.v1.core.Individual.age_at_collection', index=3,
number=4, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='age_range_at_collection', full_name='org.phenopackets.schema.v1.core.Individual.age_range_at_collection', index=4,
number=5, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='sex', full_name='org.phenopackets.schema.v1.core.Individual.sex', index=5,
number=6, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='karyotypic_sex', full_name='org.phenopackets.schema.v1.core.Individual.karyotypic_sex', index=6,
number=7, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='taxonomy', full_name='org.phenopackets.schema.v1.core.Individual.taxonomy', index=7,
number=8, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
_descriptor.OneofDescriptor(
name='age', full_name='org.phenopackets.schema.v1.core.Individual.age',
index=0, containing_type=None, fields=[]),
],
serialized_start=1448,
serialized_end=1887,
)
_BIOSAMPLE = _descriptor.Descriptor(
name='Biosample',
full_name='org.phenopackets.schema.v1.core.Biosample',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.Biosample.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='individual_id', full_name='org.phenopackets.schema.v1.core.Biosample.individual_id', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='description', full_name='org.phenopackets.schema.v1.core.Biosample.description', 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='sampled_tissue', full_name='org.phenopackets.schema.v1.core.Biosample.sampled_tissue', index=3,
number=4, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='phenotypic_features', full_name='org.phenopackets.schema.v1.core.Biosample.phenotypic_features', index=4,
number=5, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='taxonomy', full_name='org.phenopackets.schema.v1.core.Biosample.taxonomy', index=5,
number=6, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='age_of_individual_at_collection', full_name='org.phenopackets.schema.v1.core.Biosample.age_of_individual_at_collection', index=6,
number=7, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='age_range_of_individual_at_collection', full_name='org.phenopackets.schema.v1.core.Biosample.age_range_of_individual_at_collection', index=7,
number=8, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='histological_diagnosis', full_name='org.phenopackets.schema.v1.core.Biosample.histological_diagnosis', index=8,
number=9, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='tumor_progression', full_name='org.phenopackets.schema.v1.core.Biosample.tumor_progression', index=9,
number=10, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='tumor_grade', full_name='org.phenopackets.schema.v1.core.Biosample.tumor_grade', index=10,
number=11, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='diagnostic_markers', full_name='org.phenopackets.schema.v1.core.Biosample.diagnostic_markers', index=11,
number=12, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='procedure', full_name='org.phenopackets.schema.v1.core.Biosample.procedure', index=12,
number=13, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='hts_files', full_name='org.phenopackets.schema.v1.core.Biosample.hts_files', index=13,
number=14, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='variants', full_name='org.phenopackets.schema.v1.core.Biosample.variants', index=14,
number=15, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='is_control_sample', full_name='org.phenopackets.schema.v1.core.Biosample.is_control_sample', index=15,
number=16, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
_descriptor.OneofDescriptor(
name='individual_age_at_collection', full_name='org.phenopackets.schema.v1.core.Biosample.individual_age_at_collection',
index=0, containing_type=None, fields=[]),
],
serialized_start=1890,
serialized_end=2892,
)
_PROCEDURE = _descriptor.Descriptor(
name='Procedure',
full_name='org.phenopackets.schema.v1.core.Procedure',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='code', full_name='org.phenopackets.schema.v1.core.Procedure.code', index=0,
number=1, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='body_site', full_name='org.phenopackets.schema.v1.core.Procedure.body_site', index=1,
number=2, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=2895,
serialized_end=3035,
)
_AGE = _descriptor.Descriptor(
name='Age',
full_name='org.phenopackets.schema.v1.core.Age',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='age', full_name='org.phenopackets.schema.v1.core.Age.age', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=3037,
serialized_end=3055,
)
_AGERANGE = _descriptor.Descriptor(
name='AgeRange',
full_name='org.phenopackets.schema.v1.core.AgeRange',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='start', full_name='org.phenopackets.schema.v1.core.AgeRange.start', index=0,
number=1, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='end', full_name='org.phenopackets.schema.v1.core.AgeRange.end', index=1,
number=2, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=3057,
serialized_end=3171,
)
_DISEASE = _descriptor.Descriptor(
name='Disease',
full_name='org.phenopackets.schema.v1.core.Disease',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='term', full_name='org.phenopackets.schema.v1.core.Disease.term', index=0,
number=1, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='age_of_onset', full_name='org.phenopackets.schema.v1.core.Disease.age_of_onset', index=1,
number=2, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='age_range_of_onset', full_name='org.phenopackets.schema.v1.core.Disease.age_range_of_onset', index=2,
number=3, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='class_of_onset', full_name='org.phenopackets.schema.v1.core.Disease.class_of_onset', index=3,
number=4, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='tumor_stage', full_name='org.phenopackets.schema.v1.core.Disease.tumor_stage', index=4,
number=5, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
_descriptor.OneofDescriptor(
name='onset', full_name='org.phenopackets.schema.v1.core.Disease.onset',
index=0, containing_type=None, fields=[]),
],
serialized_start=3174,
serialized_end=3532,
)
_PEDIGREE_PERSON = _descriptor.Descriptor(
name='Person',
full_name='org.phenopackets.schema.v1.core.Pedigree.Person',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='family_id', full_name='org.phenopackets.schema.v1.core.Pedigree.Person.family_id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='individual_id', full_name='org.phenopackets.schema.v1.core.Pedigree.Person.individual_id', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='paternal_id', full_name='org.phenopackets.schema.v1.core.Pedigree.Person.paternal_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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='maternal_id', full_name='org.phenopackets.schema.v1.core.Pedigree.Person.maternal_id', index=3,
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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='sex', full_name='org.phenopackets.schema.v1.core.Pedigree.Person.sex', index=4,
number=5, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='affected_status', full_name='org.phenopackets.schema.v1.core.Pedigree.Person.affected_status', index=5,
number=6, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
_PEDIGREE_PERSON_AFFECTEDSTATUS,
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=3615,
serialized_end=3909,
)
_PEDIGREE = _descriptor.Descriptor(
name='Pedigree',
full_name='org.phenopackets.schema.v1.core.Pedigree',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='persons', full_name='org.phenopackets.schema.v1.core.Pedigree.persons', index=0,
number=1, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[_PEDIGREE_PERSON, ],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=3535,
serialized_end=3909,
)
_HTSFILE_INDIVIDUALTOSAMPLEIDENTIFIERSENTRY = _descriptor.Descriptor(
name='IndividualToSampleIdentifiersEntry',
full_name='org.phenopackets.schema.v1.core.HtsFile.IndividualToSampleIdentifiersEntry',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='key', full_name='org.phenopackets.schema.v1.core.HtsFile.IndividualToSampleIdentifiersEntry.key', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='value', full_name='org.phenopackets.schema.v1.core.HtsFile.IndividualToSampleIdentifiersEntry.value', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=_b('8\001'),
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=4173,
serialized_end=4241,
)
_HTSFILE = _descriptor.Descriptor(
name='HtsFile',
full_name='org.phenopackets.schema.v1.core.HtsFile',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='uri', full_name='org.phenopackets.schema.v1.core.HtsFile.uri', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='description', full_name='org.phenopackets.schema.v1.core.HtsFile.description', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='hts_format', full_name='org.phenopackets.schema.v1.core.HtsFile.hts_format', index=2,
number=3, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='genome_assembly', full_name='org.phenopackets.schema.v1.core.HtsFile.genome_assembly', index=3,
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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='individual_to_sample_identifiers', full_name='org.phenopackets.schema.v1.core.HtsFile.individual_to_sample_identifiers', index=4,
number=5, type=11, cpp_type=10, label=3,
has_default_value=False, default_value=[],
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[_HTSFILE_INDIVIDUALTOSAMPLEIDENTIFIERSENTRY, ],
enum_types=[
_HTSFILE_HTSFORMAT,
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=3912,
serialized_end=4323,
)
_GENE = _descriptor.Descriptor(
name='Gene',
full_name='org.phenopackets.schema.v1.core.Gene',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.Gene.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='alternate_ids', full_name='org.phenopackets.schema.v1.core.Gene.alternate_ids', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='symbol', full_name='org.phenopackets.schema.v1.core.Gene.symbol', 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=4325,
serialized_end=4382,
)
_VARIANT = _descriptor.Descriptor(
name='Variant',
full_name='org.phenopackets.schema.v1.core.Variant',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='hgvs_allele', full_name='org.phenopackets.schema.v1.core.Variant.hgvs_allele', index=0,
number=2, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='vcf_allele', full_name='org.phenopackets.schema.v1.core.Variant.vcf_allele', index=1,
number=3, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='spdi_allele', full_name='org.phenopackets.schema.v1.core.Variant.spdi_allele', index=2,
number=4, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='iscn_allele', full_name='org.phenopackets.schema.v1.core.Variant.iscn_allele', index=3,
number=5, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='zygosity', full_name='org.phenopackets.schema.v1.core.Variant.zygosity', index=4,
number=6, type=11, cpp_type=10, label=1,
has_default_value=False, default_value=None,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
_descriptor.OneofDescriptor(
name='allele', full_name='org.phenopackets.schema.v1.core.Variant.allele',
index=0, containing_type=None, fields=[]),
],
serialized_start=4385,
serialized_end=4740,
)
_HGVSALLELE = _descriptor.Descriptor(
name='HgvsAllele',
full_name='org.phenopackets.schema.v1.core.HgvsAllele',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.HgvsAllele.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='hgvs', full_name='org.phenopackets.schema.v1.core.HgvsAllele.hgvs', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=4742,
serialized_end=4780,
)
_VCFALLELE = _descriptor.Descriptor(
name='VcfAllele',
full_name='org.phenopackets.schema.v1.core.VcfAllele',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='vcf_version', full_name='org.phenopackets.schema.v1.core.VcfAllele.vcf_version', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='genome_assembly', full_name='org.phenopackets.schema.v1.core.VcfAllele.genome_assembly', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.VcfAllele.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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='chr', full_name='org.phenopackets.schema.v1.core.VcfAllele.chr', index=3,
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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='pos', full_name='org.phenopackets.schema.v1.core.VcfAllele.pos', index=4,
number=5, type=5, cpp_type=1, label=1,
has_default_value=False, default_value=0,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='ref', full_name='org.phenopackets.schema.v1.core.VcfAllele.ref', index=5,
number=6, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='alt', full_name='org.phenopackets.schema.v1.core.VcfAllele.alt', index=6,
number=7, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='info', full_name='org.phenopackets.schema.v1.core.VcfAllele.info', index=7,
number=8, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=4783,
serialized_end=4918,
)
_SPDIALLELE = _descriptor.Descriptor(
name='SpdiAllele',
full_name='org.phenopackets.schema.v1.core.SpdiAllele',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.SpdiAllele.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='seq_id', full_name='org.phenopackets.schema.v1.core.SpdiAllele.seq_id', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='position', full_name='org.phenopackets.schema.v1.core.SpdiAllele.position', index=2,
number=3, type=5, cpp_type=1, label=1,
has_default_value=False, default_value=0,
message_type=None, enum_type=None, containing_type=None,
is_extension=False, extension_scope=None,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='deleted_sequence', full_name='org.phenopackets.schema.v1.core.SpdiAllele.deleted_sequence', index=3,
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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='inserted_sequence', full_name='org.phenopackets.schema.v1.core.SpdiAllele.inserted_sequence', index=4,
number=5, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=4920,
serialized_end=5031,
)
_ISCNALLELE = _descriptor.Descriptor(
name='IscnAllele',
full_name='org.phenopackets.schema.v1.core.IscnAllele',
filename=None,
file=DESCRIPTOR,
containing_type=None,
fields=[
_descriptor.FieldDescriptor(
name='id', full_name='org.phenopackets.schema.v1.core.IscnAllele.id', index=0,
number=1, 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,
serialized_options=None, file=DESCRIPTOR),
_descriptor.FieldDescriptor(
name='iscn', full_name='org.phenopackets.schema.v1.core.IscnAllele.iscn', index=1,
number=2, 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,
serialized_options=None, file=DESCRIPTOR),
],
extensions=[
],
nested_types=[],
enum_types=[
],
serialized_options=None,
is_extendable=False,
syntax='proto3',
extension_ranges=[],
oneofs=[
],
serialized_start=5033,
serialized_end=5071,
)
_METADATA.fields_by_name['created'].message_type = google_dot_protobuf_dot_timestamp__pb2._TIMESTAMP
_METADATA.fields_by_name['resources'].message_type = _RESOURCE
_METADATA.fields_by_name['updates'].message_type = _UPDATE
_METADATA.fields_by_name['external_references'].message_type = _EXTERNALREFERENCE
_UPDATE.fields_by_name['timestamp'].message_type = google_dot_protobuf_dot_timestamp__pb2._TIMESTAMP
_PHENOTYPICFEATURE.fields_by_name['type'].message_type = _ONTOLOGYCLASS
_PHENOTYPICFEATURE.fields_by_name['severity'].message_type = _ONTOLOGYCLASS
_PHENOTYPICFEATURE.fields_by_name['modifiers'].message_type = _ONTOLOGYCLASS
_PHENOTYPICFEATURE.fields_by_name['age_of_onset'].message_type = _AGE
_PHENOTYPICFEATURE.fields_by_name['age_range_of_onset'].message_type = _AGERANGE
_PHENOTYPICFEATURE.fields_by_name['class_of_onset'].message_type = _ONTOLOGYCLASS
_PHENOTYPICFEATURE.fields_by_name['evidence'].message_type = _EVIDENCE
_PHENOTYPICFEATURE.oneofs_by_name['onset'].fields.append(
_PHENOTYPICFEATURE.fields_by_name['age_of_onset'])
_PHENOTYPICFEATURE.fields_by_name['age_of_onset'].containing_oneof = _PHENOTYPICFEATURE.oneofs_by_name['onset']
_PHENOTYPICFEATURE.oneofs_by_name['onset'].fields.append(
_PHENOTYPICFEATURE.fields_by_name['age_range_of_onset'])
_PHENOTYPICFEATURE.fields_by_name['age_range_of_onset'].containing_oneof = _PHENOTYPICFEATURE.oneofs_by_name['onset']
_PHENOTYPICFEATURE.oneofs_by_name['onset'].fields.append(
_PHENOTYPICFEATURE.fields_by_name['class_of_onset'])
_PHENOTYPICFEATURE.fields_by_name['class_of_onset'].containing_oneof = _PHENOTYPICFEATURE.oneofs_by_name['onset']
_EVIDENCE.fields_by_name['evidence_code'].message_type = _ONTOLOGYCLASS
_EVIDENCE.fields_by_name['reference'].message_type = _EXTERNALREFERENCE
_INDIVIDUAL.fields_by_name['date_of_birth'].message_type = google_dot_protobuf_dot_timestamp__pb2._TIMESTAMP
_INDIVIDUAL.fields_by_name['age_at_collection'].message_type = _AGE
_INDIVIDUAL.fields_by_name['age_range_at_collection'].message_type = _AGERANGE
_INDIVIDUAL.fields_by_name['sex'].enum_type = _SEX
_INDIVIDUAL.fields_by_name['karyotypic_sex'].enum_type = _KARYOTYPICSEX
_INDIVIDUAL.fields_by_name['taxonomy'].message_type = _ONTOLOGYCLASS
_INDIVIDUAL.oneofs_by_name['age'].fields.append(
_INDIVIDUAL.fields_by_name['age_at_collection'])
_INDIVIDUAL.fields_by_name['age_at_collection'].containing_oneof = _INDIVIDUAL.oneofs_by_name['age']
_INDIVIDUAL.oneofs_by_name['age'].fields.append(
_INDIVIDUAL.fields_by_name['age_range_at_collection'])
_INDIVIDUAL.fields_by_name['age_range_at_collection'].containing_oneof = _INDIVIDUAL.oneofs_by_name['age']
_BIOSAMPLE.fields_by_name['sampled_tissue'].message_type = _ONTOLOGYCLASS
_BIOSAMPLE.fields_by_name['phenotypic_features'].message_type = _PHENOTYPICFEATURE
_BIOSAMPLE.fields_by_name['taxonomy'].message_type = _ONTOLOGYCLASS
_BIOSAMPLE.fields_by_name['age_of_individual_at_collection'].message_type = _AGE
_BIOSAMPLE.fields_by_name['age_range_of_individual_at_collection'].message_type = _AGERANGE
_BIOSAMPLE.fields_by_name['histological_diagnosis'].message_type = _ONTOLOGYCLASS
_BIOSAMPLE.fields_by_name['tumor_progression'].message_type = _ONTOLOGYCLASS
_BIOSAMPLE.fields_by_name['tumor_grade'].message_type = _ONTOLOGYCLASS
_BIOSAMPLE.fields_by_name['diagnostic_markers'].message_type = _ONTOLOGYCLASS
_BIOSAMPLE.fields_by_name['procedure'].message_type = _PROCEDURE
_BIOSAMPLE.fields_by_name['hts_files'].message_type = _HTSFILE
_BIOSAMPLE.fields_by_name['variants'].message_type = _VARIANT
_BIOSAMPLE.oneofs_by_name['individual_age_at_collection'].fields.append(
_BIOSAMPLE.fields_by_name['age_of_individual_at_collection'])
_BIOSAMPLE.fields_by_name['age_of_individual_at_collection'].containing_oneof = _BIOSAMPLE.oneofs_by_name['individual_age_at_collection']
_BIOSAMPLE.oneofs_by_name['individual_age_at_collection'].fields.append(
_BIOSAMPLE.fields_by_name['age_range_of_individual_at_collection'])
_BIOSAMPLE.fields_by_name['age_range_of_individual_at_collection'].containing_oneof = _BIOSAMPLE.oneofs_by_name['individual_age_at_collection']
_PROCEDURE.fields_by_name['code'].message_type = _ONTOLOGYCLASS
_PROCEDURE.fields_by_name['body_site'].message_type = _ONTOLOGYCLASS
_AGERANGE.fields_by_name['start'].message_type = _AGE
_AGERANGE.fields_by_name['end'].message_type = _AGE
_DISEASE.fields_by_name['term'].message_type = _ONTOLOGYCLASS
_DISEASE.fields_by_name['age_of_onset'].message_type = _AGE
_DISEASE.fields_by_name['age_range_of_onset'].message_type = _AGERANGE
_DISEASE.fields_by_name['class_of_onset'].message_type = _ONTOLOGYCLASS
_DISEASE.fields_by_name['tumor_stage'].message_type = _ONTOLOGYCLASS
_DISEASE.oneofs_by_name['onset'].fields.append(
_DISEASE.fields_by_name['age_of_onset'])
_DISEASE.fields_by_name['age_of_onset'].containing_oneof = _DISEASE.oneofs_by_name['onset']
_DISEASE.oneofs_by_name['onset'].fields.append(
_DISEASE.fields_by_name['age_range_of_onset'])
_DISEASE.fields_by_name['age_range_of_onset'].containing_oneof = _DISEASE.oneofs_by_name['onset']
_DISEASE.oneofs_by_name['onset'].fields.append(
_DISEASE.fields_by_name['class_of_onset'])
_DISEASE.fields_by_name['class_of_onset'].containing_oneof = _DISEASE.oneofs_by_name['onset']
_PEDIGREE_PERSON.fields_by_name['sex'].enum_type = _SEX
_PEDIGREE_PERSON.fields_by_name['affected_status'].enum_type = _PEDIGREE_PERSON_AFFECTEDSTATUS
_PEDIGREE_PERSON.containing_type = _PEDIGREE
_PEDIGREE_PERSON_AFFECTEDSTATUS.containing_type = _PEDIGREE_PERSON
_PEDIGREE.fields_by_name['persons'].message_type = _PEDIGREE_PERSON
_HTSFILE_INDIVIDUALTOSAMPLEIDENTIFIERSENTRY.containing_type = _HTSFILE
_HTSFILE.fields_by_name['hts_format'].enum_type = _HTSFILE_HTSFORMAT
_HTSFILE.fields_by_name['individual_to_sample_identifiers'].message_type = _HTSFILE_INDIVIDUALTOSAMPLEIDENTIFIERSENTRY
_HTSFILE_HTSFORMAT.containing_type = _HTSFILE
_VARIANT.fields_by_name['hgvs_allele'].message_type = _HGVSALLELE
_VARIANT.fields_by_name['vcf_allele'].message_type = _VCFALLELE
_VARIANT.fields_by_name['spdi_allele'].message_type = _SPDIALLELE
_VARIANT.fields_by_name['iscn_allele'].message_type = _ISCNALLELE
_VARIANT.fields_by_name['zygosity'].message_type = _ONTOLOGYCLASS
_VARIANT.oneofs_by_name['allele'].fields.append(
_VARIANT.fields_by_name['hgvs_allele'])
_VARIANT.fields_by_name['hgvs_allele'].containing_oneof = _VARIANT.oneofs_by_name['allele']
_VARIANT.oneofs_by_name['allele'].fields.append(
_VARIANT.fields_by_name['vcf_allele'])
_VARIANT.fields_by_name['vcf_allele'].containing_oneof = _VARIANT.oneofs_by_name['allele']
_VARIANT.oneofs_by_name['allele'].fields.append(
_VARIANT.fields_by_name['spdi_allele'])
_VARIANT.fields_by_name['spdi_allele'].containing_oneof = _VARIANT.oneofs_by_name['allele']
_VARIANT.oneofs_by_name['allele'].fields.append(
_VARIANT.fields_by_name['iscn_allele'])
_VARIANT.fields_by_name['iscn_allele'].containing_oneof = _VARIANT.oneofs_by_name['allele']
DESCRIPTOR.message_types_by_name['MetaData'] = _METADATA
DESCRIPTOR.message_types_by_name['Update'] = _UPDATE
DESCRIPTOR.message_types_by_name['Resource'] = _RESOURCE
DESCRIPTOR.message_types_by_name['OntologyClass'] = _ONTOLOGYCLASS
DESCRIPTOR.message_types_by_name['PhenotypicFeature'] = _PHENOTYPICFEATURE
DESCRIPTOR.message_types_by_name['Evidence'] = _EVIDENCE
DESCRIPTOR.message_types_by_name['ExternalReference'] = _EXTERNALREFERENCE
DESCRIPTOR.message_types_by_name['Individual'] = _INDIVIDUAL
DESCRIPTOR.message_types_by_name['Biosample'] = _BIOSAMPLE
DESCRIPTOR.message_types_by_name['Procedure'] = _PROCEDURE
DESCRIPTOR.message_types_by_name['Age'] = _AGE
DESCRIPTOR.message_types_by_name['AgeRange'] = _AGERANGE
DESCRIPTOR.message_types_by_name['Disease'] = _DISEASE
DESCRIPTOR.message_types_by_name['Pedigree'] = _PEDIGREE
DESCRIPTOR.message_types_by_name['HtsFile'] = _HTSFILE
DESCRIPTOR.message_types_by_name['Gene'] = _GENE
DESCRIPTOR.message_types_by_name['Variant'] = _VARIANT
DESCRIPTOR.message_types_by_name['HgvsAllele'] = _HGVSALLELE
DESCRIPTOR.message_types_by_name['VcfAllele'] = _VCFALLELE
DESCRIPTOR.message_types_by_name['SpdiAllele'] = _SPDIALLELE
DESCRIPTOR.message_types_by_name['IscnAllele'] = _ISCNALLELE
DESCRIPTOR.enum_types_by_name['Sex'] = _SEX
DESCRIPTOR.enum_types_by_name['KaryotypicSex'] = _KARYOTYPICSEX
_sym_db.RegisterFileDescriptor(DESCRIPTOR)
MetaData = _reflection.GeneratedProtocolMessageType('MetaData', (_message.Message,), {
'DESCRIPTOR' : _METADATA,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.MetaData)
})
_sym_db.RegisterMessage(MetaData)
Update = _reflection.GeneratedProtocolMessageType('Update', (_message.Message,), {
'DESCRIPTOR' : _UPDATE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Update)
})
_sym_db.RegisterMessage(Update)
Resource = _reflection.GeneratedProtocolMessageType('Resource', (_message.Message,), {
'DESCRIPTOR' : _RESOURCE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Resource)
})
_sym_db.RegisterMessage(Resource)
OntologyClass = _reflection.GeneratedProtocolMessageType('OntologyClass', (_message.Message,), {
'DESCRIPTOR' : _ONTOLOGYCLASS,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.OntologyClass)
})
_sym_db.RegisterMessage(OntologyClass)
PhenotypicFeature = _reflection.GeneratedProtocolMessageType('PhenotypicFeature', (_message.Message,), {
'DESCRIPTOR' : _PHENOTYPICFEATURE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.PhenotypicFeature)
})
_sym_db.RegisterMessage(PhenotypicFeature)
Evidence = _reflection.GeneratedProtocolMessageType('Evidence', (_message.Message,), {
'DESCRIPTOR' : _EVIDENCE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Evidence)
})
_sym_db.RegisterMessage(Evidence)
ExternalReference = _reflection.GeneratedProtocolMessageType('ExternalReference', (_message.Message,), {
'DESCRIPTOR' : _EXTERNALREFERENCE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.ExternalReference)
})
_sym_db.RegisterMessage(ExternalReference)
Individual = _reflection.GeneratedProtocolMessageType('Individual', (_message.Message,), {
'DESCRIPTOR' : _INDIVIDUAL,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Individual)
})
_sym_db.RegisterMessage(Individual)
Biosample = _reflection.GeneratedProtocolMessageType('Biosample', (_message.Message,), {
'DESCRIPTOR' : _BIOSAMPLE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Biosample)
})
_sym_db.RegisterMessage(Biosample)
Procedure = _reflection.GeneratedProtocolMessageType('Procedure', (_message.Message,), {
'DESCRIPTOR' : _PROCEDURE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Procedure)
})
_sym_db.RegisterMessage(Procedure)
Age = _reflection.GeneratedProtocolMessageType('Age', (_message.Message,), {
'DESCRIPTOR' : _AGE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Age)
})
_sym_db.RegisterMessage(Age)
AgeRange = _reflection.GeneratedProtocolMessageType('AgeRange', (_message.Message,), {
'DESCRIPTOR' : _AGERANGE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.AgeRange)
})
_sym_db.RegisterMessage(AgeRange)
Disease = _reflection.GeneratedProtocolMessageType('Disease', (_message.Message,), {
'DESCRIPTOR' : _DISEASE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Disease)
})
_sym_db.RegisterMessage(Disease)
Pedigree = _reflection.GeneratedProtocolMessageType('Pedigree', (_message.Message,), {
'Person' : _reflection.GeneratedProtocolMessageType('Person', (_message.Message,), {
'DESCRIPTOR' : _PEDIGREE_PERSON,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Pedigree.Person)
})
,
'DESCRIPTOR' : _PEDIGREE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Pedigree)
})
_sym_db.RegisterMessage(Pedigree)
_sym_db.RegisterMessage(Pedigree.Person)
HtsFile = _reflection.GeneratedProtocolMessageType('HtsFile', (_message.Message,), {
'IndividualToSampleIdentifiersEntry' : _reflection.GeneratedProtocolMessageType('IndividualToSampleIdentifiersEntry', (_message.Message,), {
'DESCRIPTOR' : _HTSFILE_INDIVIDUALTOSAMPLEIDENTIFIERSENTRY,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.HtsFile.IndividualToSampleIdentifiersEntry)
})
,
'DESCRIPTOR' : _HTSFILE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.HtsFile)
})
_sym_db.RegisterMessage(HtsFile)
_sym_db.RegisterMessage(HtsFile.IndividualToSampleIdentifiersEntry)
Gene = _reflection.GeneratedProtocolMessageType('Gene', (_message.Message,), {
'DESCRIPTOR' : _GENE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Gene)
})
_sym_db.RegisterMessage(Gene)
Variant = _reflection.GeneratedProtocolMessageType('Variant', (_message.Message,), {
'DESCRIPTOR' : _VARIANT,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Variant)
})
_sym_db.RegisterMessage(Variant)
HgvsAllele = _reflection.GeneratedProtocolMessageType('HgvsAllele', (_message.Message,), {
'DESCRIPTOR' : _HGVSALLELE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.HgvsAllele)
})
_sym_db.RegisterMessage(HgvsAllele)
VcfAllele = _reflection.GeneratedProtocolMessageType('VcfAllele', (_message.Message,), {
'DESCRIPTOR' : _VCFALLELE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.VcfAllele)
})
_sym_db.RegisterMessage(VcfAllele)
SpdiAllele = _reflection.GeneratedProtocolMessageType('SpdiAllele', (_message.Message,), {
'DESCRIPTOR' : _SPDIALLELE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.SpdiAllele)
})
_sym_db.RegisterMessage(SpdiAllele)
IscnAllele = _reflection.GeneratedProtocolMessageType('IscnAllele', (_message.Message,), {
'DESCRIPTOR' : _ISCNALLELE,
'__module__' : 'base_pb2'
# @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.IscnAllele)
})
_sym_db.RegisterMessage(IscnAllele)
DESCRIPTOR._options = None
_UPDATE.fields_by_name['timestamp']._options = None
_HTSFILE_INDIVIDUALTOSAMPLEIDENTIFIERSENTRY._options = None
# @@protoc_insertion_point(module_scope)