refactor: remove full person objects outside of data description (#1503)

* refactor: remove use of Person outside of DataDescription

* fix: lost an import

* chore: missing import

* tests: fix data description to use Person again

* tests: two more mistakenly broken tests

* chore: import

* tests: few more Person() missing

* chore: bump models version

Author: dbirman

examples/aibs_smartspim_procedures.py

@@ -4,13 +4,12 @@
 
 from aind_data_schema_models.organizations import Organization
 
-from aind_data_schema.components.identifiers import Person
 from aind_data_schema.core import procedures
 from aind_data_schema.components.coordinates import CoordinateSystemLibrary
 from aind_data_schema.components.reagent import Reagent
 from aind_data_schema.components.subject_procedures import Perfusion
 
-experimenters = [Person(name="John Smith")]
+experimenters = ["John Smith"]
 # subject and specimen id can be the same?
 specimen_id = "651286"
 
@@ -39,7 +38,7 @@
 
 perfusion = procedures.Surgery(
     start_date=date(2022, 11, 17),
-    experimenters=[Person(name="LAS")],
+    experimenters=["LAS"],
     ethics_review_id="xxxx",
     protocol_id="doi_of_protocol_surgery",
     coordinate_system=CoordinateSystemLibrary.BREGMA_ARI,

examples/bergamo_ophys_acquisition.py

@@ -5,7 +5,7 @@
 from aind_data_schema_models.modalities import Modality
 from aind_data_schema_models.units import FrequencyUnit
 
-from aind_data_schema.components.identifiers import Person, Code
+from aind_data_schema.components.identifiers import Code
 from aind_data_schema.components.stimulus import PhotoStimulation, PhotoStimulationGroup
 from aind_data_schema.core.acquisition import (
     Acquisition,
@@ -69,7 +69,7 @@
 
 
 a = Acquisition(
-    experimenters=[Person(name="John Smith")],
+    experimenters=["John Smith"],
     acquisition_start_time=t,
     acquisition_end_time=t,
     subject_id="652567",

examples/data_description.py

@@ -4,19 +4,20 @@
 
 from aind_data_schema_models.modalities import Modality
 from aind_data_schema_models.organizations import Organization
+from aind_data_schema_models.data_name_patterns import DataLevel
 
-from aind_data_schema.components.identifiers import Person
 from aind_data_schema.core.data_description import Funding, DataDescription
+from aind_data_schema.components.identifiers import Person
 
 d = DataDescription(
     modalities=[Modality.ECEPHYS, Modality.BEHAVIOR_VIDEOS],
     subject_id="12345",
     creation_time=datetime(2022, 2, 21, 16, 30, 1, tzinfo=timezone.utc),
     institution=Organization.AIND,
-    investigators=[Person(name="Jane Smith")],
+    investigators=[Person(name="Daniel Birman", registry_identifier="0000-0003-3748-6289")],  # Include ORCID IDs
     funding_source=[Funding(funder=Organization.AI)],
     project_name="Example project",
-    data_level="raw",
+    data_level=DataLevel.RAW,
 )
 
 if __name__ == "__main__":

examples/ephys_acquisition.py

@@ -4,7 +4,7 @@
 
 from aind_data_schema_models.modalities import Modality
 
-from aind_data_schema.components.identifiers import Person, Software, Code
+from aind_data_schema.components.identifiers import Software, Code
 from aind_data_schema.core.acquisition import (
     Acquisition,
     StimulusEpoch,
@@ -96,7 +96,7 @@
 
 
 acquisition = Acquisition(
-    experimenters=[Person(name="John Smith")],
+    experimenters=["John Smith"],
     subject_id="664484",
     acquisition_start_time=datetime(year=2023, month=4, day=25, hour=2, minute=35, second=0, tzinfo=timezone.utc),
     acquisition_end_time=datetime(year=2023, month=4, day=25, hour=3, minute=16, second=0, tzinfo=timezone.utc),

examples/exaspim_acquisition.py

@@ -19,7 +19,6 @@
     SampleChamberConfig,
 )
 from aind_data_schema.components.coordinates import CoordinateSystemLibrary, Scale, Translation
-from aind_data_schema.components.identifiers import Person
 from aind_data_schema.components.reagent import Reagent
 from aind_data_schema.components.wrappers import AssetPath
 from aind_data_schema.core.acquisition import Acquisition, DataStream
@@ -113,7 +112,7 @@
 
 
 acq = Acquisition(
-    experimenters=[Person(name="John Smith")],
+    experimenters=["John Smith"],
     specimen_id="123456-123",
     subject_id="123456",
     instrument_id="###",

examples/fip_ophys_acquisition.py

@@ -6,7 +6,6 @@
 from aind_data_schema_models.modalities import Modality
 from aind_data_schema_models.units import TimeUnit, SizeUnit, PowerUnit, VolumeUnit
 
-from aind_data_schema.components.identifiers import Person
 from aind_data_schema.core.acquisition import (
     Acquisition,
     DataStream,
@@ -410,8 +409,8 @@
 # Create the acquisition object
 acquisition = Acquisition(
     experimenters=[
-        Person(name="Bryan MacLennan"),
-        Person(name="Kenta Hagihara"),
+        "Bryan MacLennan",
+        "Kenta Hagihara",
     ],
     subject_id="687582",
     acquisition_start_time=t_start,

examples/model.py

@@ -2,7 +2,7 @@
 
 from aind_data_schema_models.system_architecture import ModelArchitecture
 
-from aind_data_schema.components.identifiers import Code, DataAsset, Person, Software
+from aind_data_schema.components.identifiers import Code, DataAsset, Software
 from aind_data_schema.core.model import Model, ModelEvaluation, ModelTraining, PerformanceMetric
 from aind_data_schema.core.processing import ProcessStage
 import datetime
@@ -31,7 +31,7 @@
     training=[
         ModelTraining(
             stage=ProcessStage.PROCESSING,
-            experimenters=[Person(name="Dr. Dan")],
+            experimenters=["Dr. Dan"],
             code=Code(
                 input_data=[
                     DataAsset(url="s3 path to training data"),
@@ -62,7 +62,7 @@
     evaluations=[
         ModelEvaluation(
             stage=ProcessStage.PROCESSING,
-            experimenters=[Person(name="Dr. Dan")],
+            experimenters=["Dr. Dan"],
             code=Code(
                 input_data=[
                     DataAsset(url="s3 path to eval data"),

examples/mri_acquisition.py

@@ -6,7 +6,6 @@
 
 from aind_data_schema.components.coordinates import Affine, Scale, Translation, CoordinateSystemLibrary
 from aind_data_schema.components.devices import Scanner
-from aind_data_schema.components.identifiers import Person
 from aind_data_schema.core.acquisition import (
     Acquisition,
     DataStream,
@@ -80,7 +79,7 @@
     subject_id="123456",
     acquisition_start_time="2024-03-12T16:27:55.584892Z",
     acquisition_end_time="2024-03-12T16:27:55.584892Z",
-    experimenters=[Person(name="John Smith")],
+    experimenters=["John Smith"],
     protocol_id=["dx.doi.org/10.57824/protocols.io.bh7kl4n6"],
     ethics_review_id=["1234"],
     acquisition_type="3D MRI Volume",

examples/multiplane_ophys_acquisition.py

@@ -5,7 +5,6 @@
 from aind_data_schema_models.modalities import Modality
 from aind_data_schema_models.units import PowerUnit, SizeUnit, FrequencyUnit
 
-from aind_data_schema.components.identifiers import Person
 from aind_data_schema.components.coordinates import Translation, Scale, CoordinateSystemLibrary
 from aind_data_schema.core.acquisition import (
     Acquisition,
@@ -35,7 +34,7 @@
 )
 
 a = Acquisition(
-    experimenters=[Person(name="John Smith")],
+    experimenters=["John Smith"],
     acquisition_start_time=t,
     acquisition_end_time=t,
     subject_id="12345",

examples/ophys_acquisition.py

@@ -4,7 +4,6 @@
 
 from aind_data_schema_models.modalities import Modality
 
-from aind_data_schema.components.identifiers import Person
 from aind_data_schema.core.acquisition import (
     Acquisition,
     DataStream,
@@ -65,7 +64,7 @@
 ]
 
 a = Acquisition(
-    experimenters=[Person(name="Scientist Smith")],
+    experimenters=["Scientist Smith"],
     acquisition_start_time=t,
     acquisition_end_time=t,
     subject_id="652567",