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BREAKING CHANGE: updates schemas to v1.0 #1028

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Aug 20, 2024
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BREAKING CHANGE: updates schemas to v1.0 #1028

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2 changes: 1 addition & 1 deletion examples/aibs_smartspim_instrument.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",
"schema_version": "0.10.29",
"schema_version": "1.0.0",
"instrument_id": "440_SmartSPIM2_20231004",
"modification_date": "2023-10-04",
"instrument_type": "SmartSPIM",
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2 changes: 1 addition & 1 deletion examples/aibs_smartspim_procedures.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
"schema_version": "0.13.15",
"schema_version": "1.0.0",
"subject_id": "651286",
"subject_procedures": [
{
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2 changes: 1 addition & 1 deletion examples/aind_smartspim_instrument.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",
"schema_version": "0.10.29",
"schema_version": "1.0.0",
"instrument_id": "440_SmartSPIM1_20231004",
"modification_date": "2023-10-04",
"instrument_type": "SmartSPIM",
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2 changes: 1 addition & 1 deletion examples/bergamo_ophys_session.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.3.5",
"schema_version": "1.0.0",
"protocol_id": [],
"experimenter_full_name": [
"John Doe"
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2 changes: 1 addition & 1 deletion examples/data_description.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/data_description.py",
"schema_version": "0.13.12",
"schema_version": "1.0.0",
"license": "CC-BY-4.0",
"platform": {
"name": "Electrophysiology platform",
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2 changes: 1 addition & 1 deletion examples/ephys_rig.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.5.5",
"schema_version": "1.0.0",
"rig_id": "323_EPHYS1_20231003",
"modification_date": "2023-10-03",
"mouse_platform": {
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2 changes: 1 addition & 1 deletion examples/ephys_session.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.3.5",
"schema_version": "1.0.0",
"protocol_id": [],
"experimenter_full_name": [
"Max Quibble",
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2 changes: 1 addition & 1 deletion examples/exaspim_acquisition.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/acquisition.py",
"schema_version": "0.6.21",
"schema_version": "1.0.0",
"protocol_id": [],
"experimenter_full_name": [
"###"
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2 changes: 1 addition & 1 deletion examples/exaspim_instrument.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",
"schema_version": "0.10.29",
"schema_version": "1.0.0",
"instrument_id": "440_exaSPIM1-20231004",
"modification_date": "2023-10-04",
"instrument_type": "exaSPIM",
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2 changes: 1 addition & 1 deletion examples/fip_behavior_rig.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.5.5",
"schema_version": "1.0.0",
"rig_id": "447_FIP-Behavior_20000101",
"modification_date": "2000-01-01",
"mouse_platform": {
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2 changes: 1 addition & 1 deletion examples/fip_ophys_rig.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.5.5",
"schema_version": "1.0.0",
"rig_id": "428_FIP1_20231003",
"modification_date": "2023-10-03",
"mouse_platform": {
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2 changes: 1 addition & 1 deletion examples/mri_session.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.3.5",
"schema_version": "1.0.0",
"protocol_id": [
"dx.doi.org/10.57824/protocols.io.bh7kl4n6"
],
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2 changes: 1 addition & 1 deletion examples/multiplane_ophys_session.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.3.5",
"schema_version": "1.0.0",
"protocol_id": [],
"experimenter_full_name": [
"John Doe"
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2 changes: 1 addition & 1 deletion examples/ophys_procedures.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
"schema_version": "0.13.15",
"schema_version": "1.0.0",
"subject_id": "625100",
"subject_procedures": [
{
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2 changes: 1 addition & 1 deletion examples/ophys_session.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.3.5",
"schema_version": "1.0.0",
"protocol_id": [],
"experimenter_full_name": [
"John Doe"
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2 changes: 1 addition & 1 deletion examples/procedures.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
"schema_version": "0.13.15",
"schema_version": "1.0.0",
"subject_id": "625100",
"subject_procedures": [
{
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2 changes: 1 addition & 1 deletion examples/processing.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/processing.py",
"schema_version": "0.4.9",
"schema_version": "1.0.0",
"processing_pipeline": {
"data_processes": [
{
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2 changes: 1 addition & 1 deletion examples/quality_control.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/quality_metrics.py",
"schema_version": "0.0.1",
"schema_version": "1.0.0",
"overall_status": "Pass",
"overall_status_date": "2022-11-22",
"evaluations": [
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2 changes: 1 addition & 1 deletion examples/subject.json
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{
"describedBy": "https://github.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/subject.py",
"schema_version": "0.5.10",
"schema_version": "1.0.0",
"subject_id": "12345",
"sex": "Male",
"date_of_birth": "2022-11-22",
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6 changes: 3 additions & 3 deletions schemas/acquisition_schema.json
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Expand Up @@ -5144,10 +5144,10 @@
"type": "string"
},
"schema_version": {
"const": "0.6.21",
"default": "0.6.21",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.6.21"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/data_description_schema.json
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Expand Up @@ -1775,10 +1775,10 @@
"type": "string"
},
"schema_version": {
"const": "0.13.12",
"default": "0.13.12",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.13.12"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/instrument_schema.json
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Expand Up @@ -9451,10 +9451,10 @@
"type": "string"
},
"schema_version": {
"const": "0.10.29",
"default": "0.10.29",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.10.29"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/metadata_schema.json
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Expand Up @@ -558,10 +558,10 @@
"type": "string"
},
"schema_version": {
"const": "0.6.21",
"default": "0.6.21",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.6.21"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/procedures_schema.json
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Expand Up @@ -11385,10 +11385,10 @@
"type": "string"
},
"schema_version": {
"const": "0.13.15",
"default": "0.13.15",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.13.15"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/processing_schema.json
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Expand Up @@ -332,10 +332,10 @@
"type": "string"
},
"schema_version": {
"const": "0.4.9",
"default": "0.4.9",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.4.9"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/quality_control_schema.json
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Expand Up @@ -500,10 +500,10 @@
"type": "string"
},
"schema_version": {
"const": "0.0.1",
"default": "0.0.1",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.0.1"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/rig_schema.json
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Expand Up @@ -18348,10 +18348,10 @@
"type": "string"
},
"schema_version": {
"const": "0.5.5",
"default": "0.5.5",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.5.5"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/session_schema.json
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Expand Up @@ -9065,10 +9065,10 @@
"type": "string"
},
"schema_version": {
"const": "0.3.5",
"default": "0.3.5",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.3.5"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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6 changes: 3 additions & 3 deletions schemas/subject_schema.json
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Expand Up @@ -864,10 +864,10 @@
"type": "string"
},
"schema_version": {
"const": "0.5.10",
"default": "0.5.10",
"const": "1.0.0",
"default": "1.0.0",
"enum": [
"0.5.10"
"1.0.0"
],
"title": "Schema Version",
"type": "string"
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/acquisition.py
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Expand Up @@ -45,7 +45,7 @@ class Acquisition(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/acquisition.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.6.21"] = Field("0.6.21")
schema_version: Literal["1.0.0"] = Field("1.0.0")
protocol_id: List[str] = Field(default=[], title="Protocol ID", description="DOI for protocols.io")
experimenter_full_name: List[str] = Field(
...,
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/data_description.py
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Expand Up @@ -40,7 +40,7 @@ class DataDescription(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/data_description.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.13.12"] = Field("0.13.12")
schema_version: Literal["1.0.0"] = Field("1.0.0")
license: Literal["CC-BY-4.0"] = Field("CC-BY-4.0", title="License")

platform: Platform.ONE_OF = Field(
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/instrument.py
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Expand Up @@ -35,7 +35,7 @@ class Instrument(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/instrument.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.10.29"] = Field("0.10.29")
schema_version: Literal["1.0.0"] = Field("1.0.0")

instrument_id: Optional[str] = Field(
None,
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/metadata.py
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Expand Up @@ -48,7 +48,7 @@ class Metadata(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/metadata.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.2.33"] = Field("0.2.33")
schema_version: Literal["1.0.0"] = Field("1.0.0")
id: UUID = Field(
default_factory=uuid4,
alias="_id",
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/procedures.py
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Expand Up @@ -621,7 +621,7 @@ class Procedures(AindCoreModel):
_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/procedures.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})

schema_version: Literal["0.13.15"] = Field("0.13.15")
schema_version: Literal["1.0.0"] = Field("1.0.0")
subject_id: str = Field(
...,
description="Unique identifier for the subject. If this is not a Allen LAS ID, indicate this in the Notes.",
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/processing.py
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Expand Up @@ -87,7 +87,7 @@ class Processing(AindCoreModel):

_DESCRIBED_BY_URL: str = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/processing.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.4.9"] = Field("0.4.9")
schema_version: Literal["1.0.0"] = Field("1.0.0")

processing_pipeline: PipelineProcess = Field(
..., description="Pipeline used to process data", title="Processing Pipeline"
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/quality_control.py
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Expand Up @@ -36,7 +36,7 @@ class QualityControl(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/quality_metrics.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.0.1"] = Field("0.0.1")
schema_version: Literal["1.0.0"] = Field("1.0.0")
overall_status: Status = Field(..., title="Overall status")
overall_status_date: date = Field(..., title="Date of status")
evaluations: List[QCEvaluation] = Field(..., title="Evaluations")
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/rig.py
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Expand Up @@ -51,7 +51,7 @@ class Rig(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/rig.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.5.5"] = Field("0.5.5")
schema_version: Literal["1.0.0"] = Field("1.0.0")
rig_id: str = Field(
...,
description="Unique rig identifier, name convention: <room>-<apparatus name>-<date modified YYYYMMDD>",
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/session.py
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Expand Up @@ -534,7 +534,7 @@ class Session(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/session.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.3.5"] = Field("0.3.5")
schema_version: Literal["1.0.0"] = Field("1.0.0")
protocol_id: List[str] = Field([], title="Protocol ID", description="DOI for protocols.io")
experimenter_full_name: List[str] = Field(
...,
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/subject.py
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Expand Up @@ -89,7 +89,7 @@ class Subject(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/subject.py"
describedBy: str = Field(_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: Literal["0.5.10"] = Field("0.5.10")
schema_version: Literal["1.0.0"] = Field("1.0.0")
subject_id: str = Field(
...,
description="Unique identifier for the subject. If this is not a Allen LAS ID, indicate this in the Notes.",
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