aind-data-schema-models 2.4.0__tar.gz → 2.4.2__tar.gz

{aind_data_schema_models-2.4.0/src/aind_data_schema_models.egg-info → aind_data_schema_models-2.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: aind-data-schema-models
-Version: 2.4.0
+Version: 2.4.2
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT
@@ -25,6 +25,7 @@ Requires-Dist: jinja2; extra == "dev"
 Requires-Dist: pandas; extra == "dev"
 Provides-Extra: build
 Requires-Dist: aind-data-access-api[docdb]; extra == "build"
+Dynamic: license-file
 
 # aind-data-schema-models
 

aind_data_schema_models-2.4.2/src/aind_data_schema_models/__init__.py

@@ -0,0 +1,3 @@
+"""Init package"""
+
+__version__ = "2.4.2"

{aind_data_schema_models-2.4.0 → aind_data_schema_models-2.4.2}/src/aind_data_schema_models/_generators/generator.py

@@ -8,6 +8,9 @@ from pathlib import Path
 import subprocess
 
 
+SKIP_SORT = ["mouse_anatomy"]
+
+
 def check_black_version():
     """Check that the version of the black package is >= 25.0.0"""
     import black
@@ -17,6 +20,20 @@ def check_black_version():
         raise AssertionError("Please upgrade the black package to version 25.0.0 or later.")
 
 
+def load_data(data_type: str, root_path: str) -> pd.DataFrame:
+    """Load the data for the given data type"""
+
+    ROOT_DIR = Path(root_path)
+    data_file = ROOT_DIR / "_generators" / "models" / f"{data_type}.csv"
+    data = pd.read_csv(data_file)
+
+    # If there's a name field, sort A->Z
+    if "name" in data.columns and data_type not in SKIP_SORT:
+        data = data.sort_values("name")
+
+    return data
+
+
 def generate_code(data_type: str, root_path: str, isort: bool = True, black: bool = True):
     """Generate code from the template type
 
@@ -31,12 +48,10 @@ def generate_code(data_type: str, root_path: str, isort: bool = True, black: boo
     """
 
     ROOT_DIR = Path(root_path)
-    data_file = ROOT_DIR / "_generators" / "models" / f"{data_type}.csv"
     template_file = ROOT_DIR / "_generators" / "templates" / f"{data_type}.txt"
     output_file = ROOT_DIR / f"{data_type}.py"
 
-    # Load data
-    data = pd.read_csv(data_file)
+    data = load_data(data_type, root_path)
 
     # Load template
     with open(template_file) as f:

{aind_data_schema_models-2.4.0 → aind_data_schema_models-2.4.2}/src/aind_data_schema_models/_generators/models/organizations.csv

@@ -11,6 +11,7 @@ Allied,,,
 Applied Scientific Instrumentation,ASI,,
 Arecont Vision Costar,,,
 Basler,,,
+Baylor College of Medicine,BCM,ROR,02pttbw34
 Cambridge Technology,,,
 Carl Zeiss,,ROR,01xk5xs43
 Champalimaud Foundation,Champalimaud,ROR,03g001n57

{aind_data_schema_models-2.4.0 → aind_data_schema_models-2.4.2}/src/aind_data_schema_models/_generators/templates/organizations.txt

@@ -172,6 +172,7 @@ Organization.RESEARCH_INSTITUTIONS = one_of_instance(
 Organization.SUBJECT_SOURCES = one_of_instance(
     [
         Organization.AI,
+        Organization.BCM,
         Organization.COLUMBIA,
         Organization.HUST,
         Organization.JANELIA,

{aind_data_schema_models-2.4.0 → aind_data_schema_models-2.4.2}/src/aind_data_schema_models/organizations.py

@@ -127,6 +127,24 @@ class _Basler(OrganizationModel):
     registry_identifier: None = None
 
 
+class _Baylor_College_Of_Medicine(OrganizationModel):
+    """Model Baylor College of Medicine"""
+
+    name: Literal["Baylor College of Medicine"] = "Baylor College of Medicine"
+    abbreviation: Literal["BCM"] = "BCM"
+    registry: Registry.ONE_OF = Registry.ROR
+    registry_identifier: Literal["02pttbw34"] = "02pttbw34"
+
+
+class _Boston_University(OrganizationModel):
+    """Model Boston University"""
+
+    name: Literal["Boston University"] = "Boston University"
+    abbreviation: Literal["BU"] = "BU"
+    registry: Registry.ONE_OF = Registry.ROR
+    registry_identifier: Literal["05qwgg493"] = "05qwgg493"
+
+
 class _Cambridge_Technology(OrganizationModel):
     """Model Cambridge Technology"""
 
@@ -406,6 +424,15 @@ class _Janelia_Research_Campus(OrganizationModel):
     registry_identifier: Literal["013sk6x84"] = "013sk6x84"
 
 
+class _Johns_Hopkins_University(OrganizationModel):
+    """Model Johns Hopkins University"""
+
+    name: Literal["Johns Hopkins University"] = "Johns Hopkins University"
+    abbreviation: Literal["JHU"] = "JHU"
+    registry: Registry.ONE_OF = Registry.ROR
+    registry_identifier: Literal["00za53h95"] = "00za53h95"
+
+
 class _Julabo(OrganizationModel):
     """Model Julabo"""
 
@@ -442,19 +469,19 @@ class _Leica(OrganizationModel):
     registry_identifier: None = None
 
 
-class _Lumen_Dynamics(OrganizationModel):
-    """Model Lumen Dynamics"""
+class _Lifecanvas(OrganizationModel):
+    """Model LifeCanvas"""
 
-    name: Literal["Lumen Dynamics"] = "Lumen Dynamics"
+    name: Literal["LifeCanvas"] = "LifeCanvas"
     abbreviation: Literal[None] = None
     registry: None = None
     registry_identifier: None = None
 
 
-class _Lifecanvas(OrganizationModel):
-    """Model LifeCanvas"""
+class _Lumen_Dynamics(OrganizationModel):
+    """Model Lumen Dynamics"""
 
-    name: Literal["LifeCanvas"] = "LifeCanvas"
+    name: Literal["Lumen Dynamics"] = "Lumen Dynamics"
     abbreviation: Literal[None] = None
     registry: None = None
     registry_identifier: None = None
@@ -469,6 +496,15 @@ class _Mbf_Bioscience(OrganizationModel):
     registry_identifier: Literal["02zynam48"] = "02zynam48"
 
 
+class _Mit_Department_Of_Brain_And_Cognitive_Sciences(OrganizationModel):
+    """Model MIT Department of Brain and Cognitive Sciences"""
+
+    name: Literal["MIT Department of Brain and Cognitive Sciences"] = "MIT Department of Brain and Cognitive Sciences"
+    abbreviation: Literal["MIT-BCS"] = "MIT-BCS"
+    registry: None = None
+    registry_identifier: None = None
+
+
 class _Mks_Newport(OrganizationModel):
     """Model MKS Newport"""
 
@@ -487,6 +523,24 @@ class _Mpi(OrganizationModel):
     registry_identifier: None = None
 
 
+class _Massachusetts_Institute_Of_Technology(OrganizationModel):
+    """Model Massachusetts Institute of Technology"""
+
+    name: Literal["Massachusetts Institute of Technology"] = "Massachusetts Institute of Technology"
+    abbreviation: Literal["MIT"] = "MIT"
+    registry: Registry.ONE_OF = Registry.ROR
+    registry_identifier: Literal["042nb2s44"] = "042nb2s44"
+
+
+class _Mcgovern_Institute_For_Brain_Research(OrganizationModel):
+    """Model McGovern Institute for Brain Research"""
+
+    name: Literal["McGovern Institute for Brain Research"] = "McGovern Institute for Brain Research"
+    abbreviation: Literal["MIBR"] = "MIBR"
+    registry: Registry.ONE_OF = Registry.ROR
+    registry_identifier: Literal["05ymca674"] = "05ymca674"
+
+
 class _Meadowlark_Optics(OrganizationModel):
     """Model Meadowlark Optics"""
 
@@ -700,19 +754,19 @@ class _Raspberry_Pi(OrganizationModel):
     registry_identifier: None = None
 
 
-class _Same_Sky(OrganizationModel):
-    """Model Same Sky"""
+class _Sicgen(OrganizationModel):
+    """Model SICGEN"""
 
-    name: Literal["Same Sky"] = "Same Sky"
+    name: Literal["SICGEN"] = "SICGEN"
     abbreviation: Literal[None] = None
     registry: None = None
     registry_identifier: None = None
 
 
-class _Sicgen(OrganizationModel):
-    """Model SICGEN"""
+class _Same_Sky(OrganizationModel):
+    """Model Same Sky"""
 
-    name: Literal["SICGEN"] = "SICGEN"
+    name: Literal["Same Sky"] = "Same Sky"
     abbreviation: Literal[None] = None
     registry: None = None
     registry_identifier: None = None
@@ -862,6 +916,15 @@ class _Tymphany(OrganizationModel):
     registry_identifier: None = None
 
 
+class _University_Of_California_San_Diego(OrganizationModel):
+    """Model University of California, San Diego"""
+
+    name: Literal["University of California, San Diego"] = "University of California, San Diego"
+    abbreviation: Literal["UCSD"] = "UCSD"
+    registry: Registry.ONE_OF = Registry.ROR
+    registry_identifier: Literal["0168r3w48"] = "0168r3w48"
+
+
 class _Vieworks(OrganizationModel):
     """Model Vieworks"""
 
@@ -889,60 +952,6 @@ class _Ams_Osram(OrganizationModel):
     registry_identifier: Literal["045d0h266"] = "045d0h266"
 
 
-class _Mcgovern_Institute_For_Brain_Research(OrganizationModel):
-    """Model McGovern Institute for Brain Research"""
-
-    name: Literal["McGovern Institute for Brain Research"] = "McGovern Institute for Brain Research"
-    abbreviation: Literal["MIBR"] = "MIBR"
-    registry: Registry.ONE_OF = Registry.ROR
-    registry_identifier: Literal["05ymca674"] = "05ymca674"
-
-
-class _Mit_Department_Of_Brain_And_Cognitive_Sciences(OrganizationModel):
-    """Model MIT Department of Brain and Cognitive Sciences"""
-
-    name: Literal["MIT Department of Brain and Cognitive Sciences"] = "MIT Department of Brain and Cognitive Sciences"
-    abbreviation: Literal["MIT-BCS"] = "MIT-BCS"
-    registry: None = None
-    registry_identifier: None = None
-
-
-class _Massachusetts_Institute_Of_Technology(OrganizationModel):
-    """Model Massachusetts Institute of Technology"""
-
-    name: Literal["Massachusetts Institute of Technology"] = "Massachusetts Institute of Technology"
-    abbreviation: Literal["MIT"] = "MIT"
-    registry: Registry.ONE_OF = Registry.ROR
-    registry_identifier: Literal["042nb2s44"] = "042nb2s44"
-
-
-class _University_Of_California_San_Diego(OrganizationModel):
-    """Model University of California, San Diego"""
-
-    name: Literal["University of California, San Diego"] = "University of California, San Diego"
-    abbreviation: Literal["UCSD"] = "UCSD"
-    registry: Registry.ONE_OF = Registry.ROR
-    registry_identifier: Literal["0168r3w48"] = "0168r3w48"
-
-
-class _Johns_Hopkins_University(OrganizationModel):
-    """Model Johns Hopkins University"""
-
-    name: Literal["Johns Hopkins University"] = "Johns Hopkins University"
-    abbreviation: Literal["JHU"] = "JHU"
-    registry: Registry.ONE_OF = Registry.ROR
-    registry_identifier: Literal["00za53h95"] = "00za53h95"
-
-
-class _Boston_University(OrganizationModel):
-    """Model Boston University"""
-
-    name: Literal["Boston University"] = "Boston University"
-    abbreviation: Literal["BU"] = "BU"
-    registry: Registry.ONE_OF = Registry.ROR
-    registry_identifier: Literal["05qwgg493"] = "05qwgg493"
-
-
 class Organization:
     """Organization"""
 
@@ -958,6 +967,8 @@ class Organization:
     ASI = _Applied_Scientific_Instrumentation()
     ARECONT_VISION_COSTAR = _Arecont_Vision_Costar()
     BASLER = _Basler()
+    BCM = _Baylor_College_Of_Medicine()
+    BU = _Boston_University()
     CAMBRIDGE_TECHNOLOGY = _Cambridge_Technology()
     CARL_ZEISS = _Carl_Zeiss()
     CHAMPALIMAUD = _Champalimaud_Foundation()
@@ -989,15 +1000,19 @@ class Organization:
     ITEM = _Item()
     JAX = _Jackson_Laboratory()
     JANELIA = _Janelia_Research_Campus()
+    JHU = _Johns_Hopkins_University()
     JULABO = _Julabo()
     KOWA = _Kowa()
     LG = _Lg()
     LEICA = _Leica()
-    LUMEN_DYNAMICS = _Lumen_Dynamics()
     LIFECANVAS = _Lifecanvas()
+    LUMEN_DYNAMICS = _Lumen_Dynamics()
     MBF = _Mbf_Bioscience()
+    MIT_BCS = _Mit_Department_Of_Brain_And_Cognitive_Sciences()
     MKS_NEWPORT = _Mks_Newport()
     MPI = _Mpi()
+    MIT = _Massachusetts_Institute_Of_Technology()
+    MIBR = _Mcgovern_Institute_For_Brain_Research()
     MEADOWLARK_OPTICS = _Meadowlark_Optics()
     MJFF = _Michael_J_Fox_Foundation_For_Parkinson_S_Research()
     MIDOPT = _Midwest_Optical_Systems_Inc_()
@@ -1021,8 +1036,8 @@ class Organization:
     PRIZMATIX = _Prizmatix()
     QUANTIFI = _Quantifi()
     RASPBERRY_PI = _Raspberry_Pi()
-    SAME_SKY = _Same_Sky()
     SICGEN = _Sicgen()
+    SAME_SKY = _Same_Sky()
     SCHNEIDER_KREUZNACH = _Schneider_Kreuznach()
     SECOND_ORDER_EFFECTS = _Second_Order_Effects()
     SEMROCK = _Semrock()
@@ -1039,15 +1054,10 @@ class Organization:
     THORLABS = _Thorlabs()
     TRANSDUCER_TECHNIQUES = _Transducer_Techniques()
     TYMPHANY = _Tymphany()
+    UCSD = _University_Of_California_San_Diego()
     VIEWORKS = _Vieworks()
     VORTRAN = _Vortran()
     AMS_OSRAM = _Ams_Osram()
-    MIBR = _Mcgovern_Institute_For_Brain_Research()
-    MIT_BCS = _Mit_Department_Of_Brain_And_Cognitive_Sciences()
-    MIT = _Massachusetts_Institute_Of_Technology()
-    UCSD = _University_Of_California_San_Diego()
-    JHU = _Johns_Hopkins_University()
-    BU = _Boston_University()
 
     ALL = tuple(OrganizationModel.__subclasses__())
 
@@ -1187,6 +1197,7 @@ Organization.RESEARCH_INSTITUTIONS = one_of_instance(
 Organization.SUBJECT_SOURCES = one_of_instance(
     [
         Organization.AI,
+        Organization.BCM,
         Organization.COLUMBIA,
         Organization.HUST,
         Organization.JANELIA,

{aind_data_schema_models-2.4.0 → aind_data_schema_models-2.4.2/src/aind_data_schema_models.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: aind-data-schema-models
-Version: 2.4.0
+Version: 2.4.2
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT
@@ -25,6 +25,7 @@ Requires-Dist: jinja2; extra == "dev"
 Requires-Dist: pandas; extra == "dev"
 Provides-Extra: build
 Requires-Dist: aind-data-access-api[docdb]; extra == "build"
+Dynamic: license-file
 
 # aind-data-schema-models
 

{aind_data_schema_models-2.4.0 → aind_data_schema_models-2.4.2}/tests/test_generator.py

@@ -4,7 +4,7 @@ import unittest
 from unittest.mock import patch, mock_open, MagicMock
 from pathlib import Path
 import pandas as pd
-from aind_data_schema_models._generators.generator import generate_code, check_black_version
+from aind_data_schema_models._generators.generator import generate_code, check_black_version, load_data
 import os
 
 
@@ -103,6 +103,45 @@ class TestGenerateCode(unittest.TestCase):
         with patch("black.__version__", "25.0.0"):
             check_black_version()
 
+    @patch("pandas.read_csv")
+    def test_load_data(self, mock_read_csv):
+        """Test load_data function"""
+        # Mock the CSV data
+        mock_data = pd.DataFrame({"name": ["value1", "value2"], "column": ["value1", "value2"]})
+        mock_read_csv.return_value = mock_data
+
+        # Call the function
+        data = load_data("test_data", root_path="root")
+
+        # Check if the CSV file was read correctly
+        mock_read_csv.assert_called_once_with(Path("root/_generators/models/test_data.csv"))
+
+        # Check if the data was returned correctly
+        pd.testing.assert_frame_equal(data, mock_data)
+
+    @patch("pandas.read_csv")
+    def test_load_data_with_sorting(self, mock_read_csv):
+        """Test load_data function with sorting"""
+        # Mock the CSV data
+        mock_data = pd.DataFrame({"name": ["value2", "value1"], "column": ["value2", "value1"]})
+        sorted_data = mock_data.sort_values("name")
+        mock_read_csv.return_value = mock_data
+
+        # Call the function
+        data = load_data("test_data", root_path="root")
+
+        # Check if the CSV file was read correctly
+        mock_read_csv.assert_called_once_with(Path("root/_generators/models/test_data.csv"))
+
+        # Check if the data was sorted correctly
+        pd.testing.assert_frame_equal(data, sorted_data)
+
+    @patch("pandas.read_csv", side_effect=FileNotFoundError)
+    def test_load_data_missing_file(self, mock_read_csv):
+        """Test load_data function when the file is missing"""
+        with self.assertRaises(FileNotFoundError):
+            load_data("missing_data", root_path="root")
+
 
 if __name__ == "__main__":
     unittest.main()

aind_data_schema_models-2.4.0/src/aind_data_schema_models/__init__.py

@@ -1,3 +0,0 @@
-"""Init package"""
-
-__version__ = "2.4.0"

{aind_data_schema_models-2.4.0 → aind_data_schema_models-2.4.2}/src/aind_data_schema_models/process_names.py

@@ -7,10 +7,8 @@ class ProcessName(str, Enum):
     """Process names"""
 
     ANALYSIS = "Analysis"
-    PIPELINE = "Pipeline"
     COMPRESSION = "Compression"
     DENOISING = "Denoising"
-    DF_F_ESTIMATION = "dF/F estimation"
     EPHYS_CURATION = "Ephys curation"
     EPHYS_POSTPROCESSING = "Ephys postprocessing"
     EPHYS_PREPROCESSING = "Ephys preprocessing"
@@ -28,23 +26,25 @@ class ProcessName(str, Enum):
     IMAGE_FLAT_FIELD_CORRECTION = "Image flat-field correction"
     IMAGE_IMPORTING = "Image importing"
     IMAGE_MIP_VISUALIZATION = "Image mip visualization"
+    IMAGE_SPOT_DETECTION = "Image spot detection"
+    IMAGE_SPOT_SPECTRAL_UNMIXING = "Image spot spectral unmixing"
     IMAGE_THRESHOLDING = "Image thresholding"
     IMAGE_TILE_ALIGNMENT = "Image tile alignment"
     IMAGE_TILE_FUSING = "Image tile fusing"
     IMAGE_TILE_PROJECTION = "Image tile projection"
-    IMAGE_SPOT_DETECTION = "Image spot detection"
-    IMAGE_SPOT_SPECTRAL_UNMIXING = "Image spot spectral unmixing"
     MODEL_EVALUATION = "Model evaluation"
     MODEL_TRAINING = "Model training"
     NEUROPIL_SUBTRACTION = "Neuropil subtraction"
     OTHER = "Other"
+    PIPELINE = "Pipeline"
     SIMULATION = "Simulation"
     SKULL_STRIPPING = "Skull stripping"
     SPATIAL_TIMESERIES_DEMIXING = "Spatial timeseries demixing"
     SPIKE_SORTING = "Spike sorting"
-    VIDEO_MOTION_CORRECTION = "Video motion correction"
-    VIDEO_PLANE_DECROSSTALK = "Video plane decrosstalk"
     VIDEO_ROI_CLASSIFICATION = "Video ROI classification"
     VIDEO_ROI_CROSS_SESSION_MATCHING = "Video ROI cross session matching"
     VIDEO_ROI_SEGMENTATION = "Video ROI segmentation"
     VIDEO_ROI_TIMESERIES_EXTRACTION = "Video ROI timeseries extraction"
+    VIDEO_MOTION_CORRECTION = "Video motion correction"
+    VIDEO_PLANE_DECROSSTALK = "Video plane decrosstalk"
+    DF_F_ESTIMATION = "dF/F estimation"