aind-data-schema-models 0.2.2__tar.gz → 0.2.4__tar.gz

{aind_data_schema_models-0.2.2 → aind_data_schema_models-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: aind-data-schema-models
-Version: 0.2.2
+Version: 0.2.4
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT
@@ -9,6 +9,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pydantic>=2.0
+Requires-Dist: importlib-resources
 Provides-Extra: dev
 Requires-Dist: codespell; extra == "dev"
 Requires-Dist: black; extra == "dev"

{aind_data_schema_models-0.2.2 → aind_data_schema_models-0.2.4}/pyproject.toml

@@ -17,7 +17,8 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
-    "pydantic>=2.0"
+    "pydantic>=2.0",
+    "importlib-resources"
 ]
 
 [project.optional-dependencies]
@@ -38,6 +39,9 @@ where = ["src"]
 [tool.setuptools.dynamic]
 version = {attr = "aind_data_schema_models.__version__"}
 
+[tool.setuptools.package-data]
+aind_data_schema_models = ["models/*.csv"]
+
 [tool.black]
 line-length = 120
 target_version = ['py38']

aind_data_schema_models-0.2.4/src/aind_data_schema_models/__init__.py

@@ -0,0 +1,3 @@
+"""Init package"""
+
+__version__ = "0.2.4"

aind_data_schema_models-0.2.4/src/aind_data_schema_models/harp_types.py

@@ -0,0 +1,23 @@
+"""Module for Harp Device Types"""
+
+from importlib_resources import files
+from pydantic import BaseModel, ConfigDict, Field
+
+from aind_data_schema_models.utils import create_literal_class, read_csv
+
+
+class HarpDeviceTypeModel(BaseModel):
+    """Base model config"""
+
+    model_config = ConfigDict(frozen=True)
+    name: str = Field(..., title="Harp device type name")
+    whoami: int = Field(..., title="Harp whoami value")
+
+
+HarpDeviceType = create_literal_class(
+    objects=read_csv(str(files("aind_data_schema_models.models").joinpath("harp_types.csv"))),
+    class_name="HarpDeviceType",
+    base_model=HarpDeviceTypeModel,
+    discriminator="name",
+    class_module=__name__,
+)

aind_data_schema_models-0.2.4/src/aind_data_schema_models/modalities.py

@@ -0,0 +1,27 @@
+"""Module for Modality definitions"""
+
+from importlib_resources import files
+from pydantic import ConfigDict, Field
+
+from aind_data_schema_models.pid_names import BaseName
+from aind_data_schema_models.utils import create_literal_class, read_csv
+
+
+class ModalityModel(BaseName):
+    """Base model config"""
+
+    model_config = ConfigDict(frozen=True)
+    name: str = Field(..., title="Modality name")
+    abbreviation: str = Field(..., title="Modality abbreviation")
+
+
+Modality = create_literal_class(
+    objects=read_csv(str(files("aind_data_schema_models.models").joinpath("modalities.csv"))),
+    class_name="Modality",
+    base_model=ModalityModel,
+    discriminator="abbreviation",
+    class_module=__name__,
+)
+
+Modality.abbreviation_map = {m().abbreviation: m() for m in Modality.ALL}
+Modality.from_abbreviation = lambda x: Modality.abbreviation_map.get(x)

aind_data_schema_models-0.2.4/src/aind_data_schema_models/models/harp_types.csv

@@ -0,0 +1,17 @@
+name,whoami
+Behavior,1216
+Camera Controller,1168
+Clock Synchronizer,1152
+Cuttlefish,1403
+Generic Harp Device,0
+Input Expander,1106
+Lickety Split,1400
+Load Cells,1232
+Olfactometer,1140
+Sniff Detector,1401
+Sound Card,1280
+Stepper Driver,1130
+Synchronizer,1104
+Timestamp Generator Gen 1,1154
+Timestamp Generator Gen 3,1158
+Treadmill,1402

aind_data_schema_models-0.2.4/src/aind_data_schema_models/models/modalities.csv

@@ -0,0 +1,15 @@
+name,abbreviation
+Behavior,behavior
+Behavior videos,behavior-videos
+Confocal microscopy,confocal
+Electromyography,EMG
+Extracellular electrophysiology,ecephys
+Fiber photometry,fib
+Fluorescence micro-optical sectioning tomography,fMOST
+Intracellular electrophysiology,icephys
+Intrinsic signal imaging,ISI
+Magnetic resonance imaging,MRI
+Multiplexed error-robust fluorescence in situ hybridization,merfish
+Planar optical physiology,pophys
+Scanned line projection imaging,slap
+Selective plane illumination microscopy,SPIM

aind_data_schema_models-0.2.4/src/aind_data_schema_models/models/organizations.csv

@@ -0,0 +1,90 @@
+name,abbreviation,registry_abbreviation,registry_identifier
+AA Opto Electronic,,,
+ASUS,,ROR,00bxkz165
+Abcam,,ROR,02e1wjw63
+Addgene,,ROR,01nn1pw54
+Ailipu Technology Co,Ailipu,,
+Allen Institute,AI,ROR,03cpe7c52
+Allen Institute for Brain Science,AIBS,ROR,00dcv1019
+Allen Institute for Neural Dynamics,AIND,ROR,04szwah67
+Allied,,,
+Applied Scientific Instrumentation,ASI,,
+Arecont Vision Costar,,,
+Basler,,,
+Cambridge Technology,,,
+Carl Zeiss,,ROR,01xk5xs43
+Champalimaud Foundation,Champalimaud,ROR,03g001n57
+Chan Zuckerberg Initiative,CZI,ROR,02qenvm24
+Chroma,,,
+Coherent Scientific,,ROR,031tysd23
+Columbia University,Columbia,ROR,00hj8s172
+Computar,,,
+Conoptics,,,
+Custom,,,
+Dodotronic,,,
+Doric,,ROR,059n53q30
+Ealing,,,
+Edmund Optics,,ROR,01j1gwp17
+Emory University,Emory,ROR,03czfpz43
+Euresys,,,
+Fujinon,,,
+Hamamatsu,,ROR,03natb733
+Hamilton,,,
+Huazhong University of Science and Technology,HUST,ROR,00p991c53
+IR Robot Co,,,
+ISL Products International,ISL,,
+Infinity Photo-Optical,,,
+Integrated DNA Technologies,IDT,ROR,009jvpf03
+Interuniversity Microelectronics Center,IMEC,ROR,02kcbn207
+Invitrogen,,ROR,03x1ewr52
+Jackson Laboratory,JAX,ROR,021sy4w91
+Janelia Research Campus,Janelia,ROR,013sk6x84
+Julabo,,,
+LG,,ROR,02b948n83
+Leica,,,
+Lumen Dynamics,,,
+LifeCanvas,,,
+MBF Bioscience,MBF,ROR,02zynam48
+MKS Newport,,ROR,00k17f049
+MPI,MPI,,
+Meadowlark Optics,,ROR,00n8qbq54
+Michael J. Fox Foundation for Parkinson's Research,MJFF,ROR,03arq3225
+"Midwest Optical Systems, Inc.",MidOpt,,
+Mitutuyo,,,
+NResearch Inc,,,
+National Center for Complementary and Integrative Health,NCCIH,ROR,00190t495
+National Institute of Mental Health,NIMH,ROR,04xeg9z08
+National Institute of Neurological Disorders and Stroke,NINDS,ROR,01s5ya894
+National Instruments,,ROR,026exqw73
+Navitar,,,
+Neurophotometrics,,,
+New Scale Technologies,,,
+New York University,NYU,ROR,0190ak572
+Nikon,,ROR,0280y9h11
+Olympus,,ROR,02vcdte90
+Open Ephys Production Site,OEPS,ROR,007rkz355
+Optotune,,,
+Other,,,
+Oxxius,,,
+Prizmatix,,,
+Quantifi,,,
+Raspberry Pi,,,
+SICGEN,,,
+Schneider-Kreuznach,,,
+Second Order Effects,,,
+Semrock,,,
+Sigma-Aldritch,,,
+Simons Foundation,,ROR,01cmst727
+Spinnaker,,,
+Tamron,,,
+Technical Manufacturing Corporation,TMC,,
+Teledyne FLIR,FLIR,ROR,01j1gwp17
+Templeton World Charity Foundation,TWCF,ROR,00x0z1472
+The Imaging Source,,,
+The Lee Company,,,
+Thermo Fisher Scientific,,ROR,03x1ewr52
+Thorlabs,,ROR,04gsnvb07
+Tymphany,,,
+Vieworks,,,
+Vortran,,,
+ams OSRAM,,ROR,045d0h266

aind_data_schema_models-0.2.4/src/aind_data_schema_models/models/platforms.csv

@@ -0,0 +1,17 @@
+name,abbreviation
+Behavior platform,behavior
+Confocal microscopy platform,confocal
+Electrophysiology platform,ecephys
+ExaSPIM platform,exaSPIM
+Frame-projected independent-fiber photometry platform,FIP
+Hybridization chain reaction platform,HCR
+Hyperspectral fiber photometry platform,HSFP
+Intrinsic signal imaging platform,ISI
+MERFISH platform,MERFISH
+Magnetic resonance imaging platform,MRI
+MesoSPIM platform,mesoSPIM
+Motor observatory platform,motor-observatory
+Multiplane optical physiology platform,multiplane-ophys
+SLAP2 platform,SLAP2
+Single-plane optical physiology platform,single-plane-ophys
+SmartSPIM platform,SmartSPIM

aind_data_schema_models-0.2.4/src/aind_data_schema_models/models/process_names.csv

@@ -0,0 +1,38 @@
+name
+Analysis
+Compression
+Denoising
+dF/F estimation
+Ephys curation
+Ephys postprocessing
+Ephys preprocessing
+Ephys visualization
+Fiducial segmentation
+File format conversion
+Fluorescence event detection
+Image atlas alignment
+Image background subtraction
+Image cell classification
+Image cell quantification
+Image cell segmentation
+Image destriping
+Image flat-field correction
+Image importing
+Image mip visualization
+Image thresholding
+Image tile alignment
+Image tile fusing
+Image tile projection
+Manual annotation
+Neuropil subtraction
+Other
+Quality control and assessment
+Simulation
+Skull stripping
+Spatial timeseries demixing
+Spike sorting
+Video motion correction
+Video plane decrosstalk
+Video ROI classification
+Video ROI segmentation
+Video ROI timeseries extraction

aind_data_schema_models-0.2.4/src/aind_data_schema_models/models/registries.csv

@@ -0,0 +1,8 @@
+name,abbreviation
+Addgene,ADDGENE
+Edinburgh Mouse Atlas Project,EMAPA
+Mouse Genome Informatics,MGI
+National Center for Biotechnology Information,NCBI
+Open Researcher and Contributor ID,ORCID
+Research Organization Registry,ROR
+Research Resource Identifiers,RRID

aind_data_schema_models-0.2.4/src/aind_data_schema_models/models/species.csv

@@ -0,0 +1,6 @@
+name,registry_abbreviation,registry_identifier
+Callithrix jacchus,NCBI,NCBI:txid9483
+Homo sapiens,NCBI,NCBI:txid9606
+Macaca mulatta,NCBI,NCBI:txid9544
+Mus musculus,NCBI,NCBI:txid10090
+Rattus norvegicus,NCBI,NCBI:txid10116

aind_data_schema_models-0.2.4/src/aind_data_schema_models/models/specimen_procedure_types.csv

@@ -0,0 +1,19 @@
+name
+Clearing
+Delipidation
+Embedding
+Expansion
+Fixation
+Fixation and permeabilization
+Gelation
+Hybridication and amplification
+Hybridization Chain Reaction
+Immunolabeling
+Mounting
+Other
+Refractive index matching
+Sectioning
+Soak
+Storage
+Stripping
+Tamoxifen induction

aind_data_schema_models-0.2.4/src/aind_data_schema_models/organizations.py

@@ -0,0 +1,152 @@
+"""Module for Organization definitions, including manufacturers, institutions, and vendors"""
+
+from importlib_resources import files
+from pydantic import BaseModel, ConfigDict
+
+from aind_data_schema_models.registries import RegistryModel, map_registry
+from aind_data_schema_models.utils import create_literal_class, one_of_instance, read_csv
+
+
+class OrganizationModel(BaseModel):
+    """Base model config"""
+
+    model_config = ConfigDict(frozen=True)
+
+    name: str
+    abbreviation: str = None
+    registry: RegistryModel = None
+    registry_identifier: str = None
+
+
+Organization = create_literal_class(
+    objects=read_csv(str(files("aind_data_schema_models.models").joinpath("organizations.csv"))),
+    class_name="Organization",
+    base_model=OrganizationModel,
+    discriminator="name",
+    field_handlers={"registry_abbreviation": map_registry},
+    class_module=__name__,
+)
+
+Organization.abbreviation_map = {m().abbreviation: m() for m in Organization.ALL}
+Organization.name_map = {m().name: m() for m in Organization.ALL}
+Organization.from_abbreviation = lambda x: Organization.abbreviation_map.get(x)
+Organization.from_name = lambda x: Organization.name_map.get(x)
+
+
+Organization.DETECTOR_MANUFACTURERS = one_of_instance(
+    [
+        Organization.AILIPU,
+        Organization.ALLIED,
+        Organization.BASLER,
+        Organization.DODOTRONIC,
+        Organization.EDMUND_OPTICS,
+        Organization.HAMAMATSU,
+        Organization.SPINNAKER,
+        Organization.FLIR,
+        Organization.THE_IMAGING_SOURCE,
+        Organization.THORLABS,
+        Organization.VIEWORKS,
+        Organization.OTHER,
+    ]
+)
+
+Organization.FILTER_MANUFACTURERS = one_of_instance(
+    [
+        Organization.CHROMA,
+        Organization.EDMUND_OPTICS,
+        Organization.MIDOPT,
+        Organization.SEMROCK,
+        Organization.THORLABS,
+        Organization.OTHER,
+    ]
+)
+
+Organization.LENS_MANUFACTURERS = one_of_instance(
+    [
+        Organization.COMPUTAR,
+        Organization.EDMUND_OPTICS,
+        Organization.FUJINON,
+        Organization.HAMAMATSU,
+        Organization.INFINITY_PHOTO_OPTICAL,
+        Organization.LEICA,
+        Organization.MITUTUYO,
+        Organization.NAVITAR,
+        Organization.NIKON,
+        Organization.OLYMPUS,
+        Organization.SCHNEIDER_KREUZNACH,
+        Organization.THORLABS,
+        Organization.CARL_ZEISS,
+        Organization.OTHER,
+    ]
+)
+
+Organization.DAQ_DEVICE_MANUFACTURERS = one_of_instance(
+    [
+        Organization.AIND,
+        Organization.CHAMPALIMAUD,
+        Organization.NATIONAL_INSTRUMENTS,
+        Organization.IMEC,
+        Organization.OEPS,
+        Organization.SECOND_ORDER_EFFECTS,
+        Organization.OTHER,
+    ]
+)
+
+Organization.LASER_MANUFACTURERS = one_of_instance(
+    [
+        Organization.COHERENT_SCIENTIFIC,
+        Organization.HAMAMATSU,
+        Organization.OXXIUS,
+        Organization.QUANTIFI,
+        Organization.VORTRAN,
+        Organization.OTHER,
+    ]
+)
+
+Organization.LED_MANUFACTURERS = one_of_instance(
+    [Organization.AMS_OSRAM, Organization.DORIC, Organization.PRIZMATIX, Organization.THORLABS, Organization.OTHER]
+)
+
+Organization.MANIPULATOR_MANUFACTURERS = one_of_instance([Organization.NEW_SCALE_TECHNOLOGIES, Organization.OTHER])
+
+Organization.MONITOR_MANUFACTURERS = one_of_instance([Organization.ASUS, Organization.LG, Organization.OTHER])
+
+Organization.SPEAKER_MANUFACTURERS = one_of_instance([Organization.TYMPHANY, Organization.ISL, Organization.OTHER])
+
+Organization.FUNDERS = one_of_instance(
+    [
+        Organization.AI,
+        Organization.CZI,
+        Organization.MBF,
+        Organization.MJFF,
+        Organization.NCCIH,
+        Organization.NIMH,
+        Organization.NINDS,
+        Organization.SIMONS_FOUNDATION,
+        Organization.TWCF,
+    ]
+)
+
+Organization.RESEARCH_INSTITUTIONS = one_of_instance(
+    [
+        Organization.AIBS,
+        Organization.AIND,
+        Organization.COLUMBIA,
+        Organization.HUST,
+        Organization.JANELIA,
+        Organization.NYU,
+        Organization.OTHER,
+    ]
+)
+
+Organization.SUBJECT_SOURCES = one_of_instance(
+    [
+        Organization.AI,
+        Organization.COLUMBIA,
+        Organization.HUST,
+        Organization.JANELIA,
+        Organization.JAX,
+        Organization.NYU,
+        Organization.OTHER,
+    ]
+)

aind_data_schema_models-0.2.4/src/aind_data_schema_models/platforms.py

@@ -0,0 +1,27 @@
+"""Module for Platform definitions"""
+
+from importlib_resources import files
+from pydantic import BaseModel, ConfigDict, Field
+
+from aind_data_schema_models.utils import create_literal_class, read_csv
+
+
+class PlatformModel(BaseModel):
+    """Base model config"""
+
+    model_config = ConfigDict(frozen=True)
+
+    name: str = Field(..., title="Platform name")
+    abbreviation: str = Field(..., title="Platform abbreviation")
+
+
+Platform = create_literal_class(
+    objects=read_csv(str(files("aind_data_schema_models.models").joinpath("platforms.csv"))),
+    class_name="Platform",
+    base_model=PlatformModel,
+    discriminator="name",
+    class_module=__name__,
+)
+
+Platform.abbreviation_map = {p().abbreviation: p() for p in Platform.ALL}
+Platform.from_abbreviation = lambda x: Platform.abbreviation_map.get(x)

aind_data_schema_models-0.2.4/src/aind_data_schema_models/process_names.py

@@ -0,0 +1,9 @@
+"""Module for process names definitions"""
+
+from importlib_resources import files
+
+from aind_data_schema_models.utils import create_string_enum, read_csv
+
+ProcessName = create_string_enum(
+    name="ProcessName", objects=read_csv(str(files("aind_data_schema_models.models").joinpath("process_names.csv")))
+)

aind_data_schema_models-0.2.4/src/aind_data_schema_models/registries.py

@@ -0,0 +1,40 @@
+"""Common registries"""
+
+from typing import Union
+
+from importlib_resources import files
+from pydantic import ConfigDict, Field
+from typing_extensions import Annotated
+
+from aind_data_schema_models.pid_names import BaseName
+from aind_data_schema_models.utils import create_literal_class, read_csv
+
+
+class RegistryModel(BaseName):
+    """Base model config"""
+
+    model_config = ConfigDict(frozen=True)
+
+    name: str = Field(..., title="Registry name")
+    abbreviation: str = Field(..., title="Registry abbreviation")
+
+
+Registry = create_literal_class(
+    objects=read_csv(str(files("aind_data_schema_models.models").joinpath("registries.csv"))),
+    class_name="Registry",
+    base_model=RegistryModel,
+    discriminator="abbreviation",
+    class_module=__name__,
+)
+
+Registry.abbreviation_map = {m().abbreviation: m() for m in Registry.ALL}
+Registry.from_abbreviation = lambda x: Registry.abbreviation_map.get(x)
+
+
+def map_registry(abbreviation: str, record: dict):
+    """replace the "registry" key of a dictionary with a RegistryModel object"""
+    registry = Registry.from_abbreviation(abbreviation)
+    if registry:
+        record["registry"] = Annotated[Union[type(registry)], Field(default=registry, discriminator="name")]
+    else:
+        record["registry"] = Annotated[None, Field(None)]

aind_data_schema_models-0.2.4/src/aind_data_schema_models/species.py

@@ -0,0 +1,27 @@
+"""Module for species definitions"""
+
+from importlib_resources import files
+from pydantic import BaseModel, ConfigDict, Field
+
+from aind_data_schema_models.registries import RegistryModel, map_registry
+from aind_data_schema_models.utils import create_literal_class, read_csv
+
+
+class SpeciesModel(BaseModel):
+    """base model for species, like Mus musculus"""
+
+    model_config = ConfigDict(frozen=True)
+
+    name: str = Field(..., title="Species name")
+    registry: RegistryModel = Field(..., title="Species registry")
+    registry_identifier: str = Field(..., title="Species registry identifier")
+
+
+Species = create_literal_class(
+    objects=read_csv(str(files("aind_data_schema_models.models").joinpath("species.csv"))),
+    class_name="Species",
+    base_model=SpeciesModel,
+    discriminator="name",
+    field_handlers={"registry_abbreviation": map_registry},
+    class_module=__name__,
+)

aind_data_schema_models-0.2.4/src/aind_data_schema_models/specimen_procedure_types.py

@@ -0,0 +1,10 @@
+"""Script for the SpecimenProcedureType enum class."""
+
+from importlib_resources import files
+
+from aind_data_schema_models.utils import create_string_enum, read_csv
+
+SpecimenProcedureType = create_string_enum(
+    name="SpecimenProcedureType",
+    objects=read_csv(files("aind_data_schema_models.models").joinpath("specimen_procedure_types.csv")),
+)