fiber core diameter, rig_id description (#785)

saskiad · web-flow · commit a18ed5068ced · 2024-02-23T07:53:45.000-08:00
diff --git a/examples/aibs_smartspim_instrument.json b/examples/aibs_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",
-   "schema_version": "0.10.10",
+   "schema_version": "0.10.11",
    "instrument_id": "SmartSPIM2-2",
    "modification_date": "2023-10-04",
    "instrument_type": "SmartSPIM",
diff --git a/examples/aibs_smartspim_procedures.json b/examples/aibs_smartspim_procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "0.12.4",
+   "schema_version": "0.12.5",
    "subject_id": "651286",
    "subject_procedures": [
       {
diff --git a/examples/ephys_rig.json b/examples/ephys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
-   "schema_version": "0.2.15",
+   "schema_version": "0.2.16",
    "rig_id": "323_EPHYS1",
    "modification_date": "2023-10-03",
    "mouse_platform": {
diff --git a/examples/exaspim_instrument.json b/examples/exaspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",
-   "schema_version": "0.10.10",
+   "schema_version": "0.10.11",
    "instrument_id": "exaSPIM1-1",
    "modification_date": "2023-10-04",
    "instrument_type": "exaSPIM",
diff --git a/examples/fip_ophys_rig.json b/examples/fip_ophys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
-   "schema_version": "0.2.15",
+   "schema_version": "0.2.16",
    "rig_id": "428_FIP1_2",
    "modification_date": "2023-10-03",
    "mouse_platform": {
diff --git a/examples/ophys_procedures.json b/examples/ophys_procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "0.12.4",
+   "schema_version": "0.12.5",
    "subject_id": "625100",
    "subject_procedures": [
       {
@@ -88,7 +88,7 @@
                         "additional_settings": {},
                         "notes": null,
                         "core_diameter": "200",
-                        "core_diameter_unit": "um",
+                        "core_diameter_unit": "micrometer",
                         "numerical_aperture": "0.37",
                         "ferrule_material": "Ceramic",
                         "active_length": null,
diff --git a/examples/procedures.json b/examples/procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "0.12.4",
+   "schema_version": "0.12.5",
    "subject_id": "625100",
    "subject_procedures": [
       {
diff --git a/src/aind_data_schema/core/instrument.py b/src/aind_data_schema/core/instrument.py
@@ -35,11 +35,11 @@ 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["0.10.10"] = Field("0.10.10")
+    schema_version: Literal["0.10.11"] = Field("0.10.11")
 
     instrument_id: Optional[str] = Field(
         None,
-        description="Unique identifier for this instrument. Naming convention: <room>-<apparatus>-<version>",
+        description="Unique identifier for this instrument. Naming convention: <room>-<apparatus>-<date modified>",
         title="Instrument ID",
     )
     modification_date: date = Field(..., title="Date of modification")
diff --git a/src/aind_data_schema/core/metadata.py b/src/aind_data_schema/core/metadata.py
@@ -46,7 +46,7 @@ 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["0.1.30"] = Field("0.1.30")
+    schema_version: Literal["0.1.31"] = Field("0.1.31")
     id: UUID = Field(
         default_factory=uuid4,
         alias="_id",
diff --git a/src/aind_data_schema/core/procedures.py b/src/aind_data_schema/core/procedures.py
@@ -573,7 +573,7 @@ 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["0.12.4"] = Field("0.12.4", description="schema version", title="Version")
+    schema_version: Literal["0.12.5"] = Field("0.12.5", description="schema version", title="Version")
     subject_id: str = Field(
         ...,
         description="Unique identifier for the subject. If this is not a Allen LAS ID, indicate this in the Notes.",
diff --git a/src/aind_data_schema/core/rig.py b/src/aind_data_schema/core/rig.py
@@ -49,8 +49,8 @@ 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["0.2.15"] = Field("0.2.15")
-    rig_id: str = Field(..., description="room_stim apparatus_version", title="Rig ID")
+    schema_version: Literal["0.2.16"] = Field("0.2.16")
+    rig_id: str = Field(..., description="room_rig name_date modified", title="Rig ID")
     modification_date: date = Field(..., title="Date of modification")
     mouse_platform: MOUSE_PLATFORMS
     stimulus_devices: List[STIMULUS_DEVICES] = Field(default=[], title="Stimulus devices")
diff --git a/src/aind_data_schema/models/devices.py b/src/aind_data_schema/models/devices.py
@@ -571,7 +571,7 @@ class FiberProbe(Device):
     device_type: Literal["Fiber optic probe"] = "Fiber optic probe"
     core_diameter: Decimal = Field(..., title="Core diameter (um)")
     #  TODO: Check if this should be an enum?
-    core_diameter_unit: str = Field("um", title="Core diameter unit")
+    core_diameter_unit: SizeUnit = Field(SizeUnit.UM, title="Core diameter unit")
     numerical_aperture: Decimal = Field(..., title="Numerical aperture")
     ferrule_material: Optional[FerruleMaterial] = Field(None, title="Ferrule material")
     active_length: Optional[Decimal] = Field(None, title="Active length (mm)", description="Length of taper")

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",`
`3`		`- "schema_version": "0.10.10",`
	`3`	`+ "schema_version": "0.10.11",`
`4`	`4`	`"instrument_id": "SmartSPIM2-2",`
`5`	`5`	`"modification_date": "2023-10-04",`
`6`	`6`	`"instrument_type": "SmartSPIM",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",`
`3`		`- "schema_version": "0.12.4",`
	`3`	`+ "schema_version": "0.12.5",`
`4`	`4`	`"subject_id": "651286",`
`5`	`5`	`"subject_procedures": [`
`6`	`6`	`{`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",`
`3`		`- "schema_version": "0.2.15",`
	`3`	`+ "schema_version": "0.2.16",`
`4`	`4`	`"rig_id": "323_EPHYS1",`
`5`	`5`	`"modification_date": "2023-10-03",`
`6`	`6`	`"mouse_platform": {`