Feat 952 examples generator (#959)

Sun-flow · web-flow · commit 319bdcb64157 · 2024-06-11T14:53:22.000Z
* adding output directory to example generation files

* initial commit

* Update examples_generator.py

* linters

* updating aind-data-schema-models pin

* class-based implementation

* initial commit

* Update test_examples_generator.py

* linters

* logging

* patching out write calls
diff --git a/examples/aibs_smartspim_instrument.py b/examples/aibs_smartspim_instrument.py
@@ -16,6 +16,8 @@
 )
 from aind_data_schema.core.instrument import Com, Instrument
 
+OUTPUT_PATH = "examples/"
+
 inst = Instrument(
     instrument_id="440_SmartSPIM2_20231004",
     modification_date=datetime.date(2023, 10, 4),
@@ -211,4 +213,4 @@
 )
 serialized = inst.model_dump_json()
 deserialized = Instrument.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="aibs_smartspim")
+deserialized.write_standard_file(prefix="aibs_smartspim", output_directory=OUTPUT_PATH)
diff --git a/examples/aibs_smartspim_procedures.py b/examples/aibs_smartspim_procedures.py
@@ -6,6 +6,8 @@
 
 from aind_data_schema.core import procedures
 
+OUTPUT_PATH = "examples/"
+
 experimenter = "John Smith"
 # subject and specimen id can be the same?
 specimen_id = "651286"
@@ -161,4 +163,4 @@
 
 serialized = all_procedures.model_dump_json()
 deserialized = procedures.Procedures.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="aibs_smartspim")
+deserialized.write_standard_file(prefix="aibs_smartspim", output_directory=OUTPUT_PATH)
diff --git a/examples/aind_smartspim_instrument.py b/examples/aind_smartspim_instrument.py
@@ -7,6 +7,8 @@
 from aind_data_schema.components.devices import Filter, Laser, MotorizedStage, OpticalTable, ScanningStage
 from aind_data_schema.core.instrument import Com, Detector, Instrument, Objective
 
+OUTPUT_PATH = "examples/"
+
 inst = Instrument(
     instrument_id="440_SmartSPIM1_20231004",
     instrument_type="SmartSPIM",
@@ -255,4 +257,4 @@
 
 serialized = inst.model_dump_json()
 deserialized = Instrument.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="aind_smartspim")
+deserialized.write_standard_file(prefix="aind_smartspim", output_directory=OUTPUT_PATH)
diff --git a/examples/bergamo_ophys_session.py b/examples/bergamo_ophys_session.py
@@ -15,6 +15,8 @@
     Stream,
 )
 
+OUTPUT_PATH = "examples/"
+
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 7, 12, 7, 00, 00, tzinfo=timezone.utc)
@@ -107,4 +109,4 @@
 
 serialized = s.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="bergamo_ophys")
+deserialized.write_standard_file(prefix="bergamo_ophys", output_directory=OUTPUT_PATH)
diff --git a/examples/data_description.py b/examples/data_description.py
@@ -9,6 +9,8 @@
 
 from aind_data_schema.core.data_description import Funding, RawDataDescription
 
+OUTPUT_PATH = "examples/"
+
 d = RawDataDescription(
     modality=[Modality.ECEPHYS, Modality.BEHAVIOR_VIDEOS],
     platform=Platform.ECEPHYS,
@@ -21,4 +23,4 @@
 
 serialized = d.model_dump_json()
 deserialized = RawDataDescription.model_validate_json(serialized)
-deserialized.write_standard_file()
+deserialized.write_standard_file(output_directory=OUTPUT_PATH)
diff --git a/examples/ephys_rig.py b/examples/ephys_rig.py
@@ -28,6 +28,8 @@
 )
 from aind_data_schema.core.rig import Rig
 
+OUTPUT_PATH = "examples/"
+
 # Describes a rig with running wheel, 2 behavior cameras, one Harp Behavior board,
 # one dual-color laser module, one stick microscope, and 2 Neuropixels probes
 
@@ -213,4 +215,4 @@
 )
 serialized = rig.model_dump_json()
 deserialized = Rig.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="ephys")
+deserialized.write_standard_file(prefix="ephys", output_directory=OUTPUT_PATH)
diff --git a/examples/ephys_session.py b/examples/ephys_session.py
@@ -17,6 +17,8 @@
     VisualStimulation,
 )
 
+OUTPUT_PATH = "examples/"
+
 session = Session(
     experimenter_full_name=["Max Quibble", "Finn Tickle"],
     subject_id="664484",
@@ -221,4 +223,4 @@
 
 serialized = session.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="ephys")
+deserialized.write_standard_file(prefix="ephys", output_directory=OUTPUT_PATH)
diff --git a/examples/exaspim_acquisition.py b/examples/exaspim_acquisition.py
@@ -13,6 +13,8 @@
 from aind_data_schema.core import acquisition
 from aind_data_schema.core.procedures import Reagent
 
+OUTPUT_PATH = "examples/"
+
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 11, 22, 8, 43, 00, tzinfo=timezone.utc)
@@ -113,4 +115,4 @@
 
 serialized = acq.model_dump_json()
 deserialized = acquisition.Acquisition.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="exaspim")
+deserialized.write_standard_file(prefix="exaspim", output_directory=OUTPUT_PATH)
diff --git a/examples/exaspim_instrument.py b/examples/exaspim_instrument.py
@@ -7,6 +7,8 @@
 from aind_data_schema.components.devices import DAQChannel, DAQDevice, Detector, Filter, Laser
 from aind_data_schema.core import instrument
 
+OUTPUT_PATH = "examples/"
+
 inst = instrument.Instrument(
     instrument_id="440_exaSPIM1-20231004",
     instrument_type="exaSPIM",
@@ -205,4 +207,4 @@
 )
 serialized = inst.model_dump_json()
 deserialized = instrument.Instrument.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="exaspim")
+deserialized.write_standard_file(prefix="exaspim", output_directory=OUTPUT_PATH)
diff --git a/examples/fip_behavior_rig.py b/examples/fip_behavior_rig.py
@@ -8,6 +8,8 @@
 import aind_data_schema.components.devices as d
 import aind_data_schema.core.rig as r
 
+OUTPUT_PATH = "examples/"
+
 r = r.Rig(
     rig_id="447_FIP_Behavior_20000101",
     modification_date=date(2000, 1, 1),
@@ -340,4 +342,4 @@
     ],
 )
 
-r.write_standard_file(prefix="fip_behavior")
+r.write_standard_file(prefix="fip_behavior", output_directory=OUTPUT_PATH)
diff --git a/examples/fip_ophys_rig.py b/examples/fip_ophys_rig.py
@@ -7,6 +7,8 @@
 import aind_data_schema.components.devices as d
 import aind_data_schema.core.rig as r
 
+OUTPUT_PATH = "examples/"
+
 rig = r.Rig(
     rig_id="428_FIP1_20231003",
     modification_date=date(2023, 10, 3),
@@ -284,4 +286,4 @@
 )
 serialized = rig.model_dump_json()
 deserialized = r.Rig.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="fip_ophys")
+deserialized.write_standard_file(prefix="fip_ophys", output_directory=OUTPUT_PATH)
diff --git a/examples/mri_session.py b/examples/mri_session.py
@@ -8,6 +8,8 @@
 from aind_data_schema.components.devices import Scanner
 from aind_data_schema.core.session import MRIScan, MriScanSequence, ScanType, Session, Stream, SubjectPosition
 
+OUTPUT_PATH = "examples/"
+
 scan1 = MRIScan(
     scan_index="1",
     mri_scanner=Scanner(
@@ -74,4 +76,4 @@
 )
 serialized = sess.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="mri")
+deserialized.write_standard_file(prefix="mri", output_directory=OUTPUT_PATH)
diff --git a/examples/multiplane_ophys_session.py b/examples/multiplane_ophys_session.py
@@ -7,6 +7,8 @@
 
 from aind_data_schema.core.session import FieldOfView, LaserConfig, Session, Stream
 
+OUTPUT_PATH = "examples/"
+
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 7, 12, 7, 00, 00, tzinfo=timezone.utc)
@@ -202,4 +204,4 @@
 )
 serialized = s.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="multiplane_ophys")
+deserialized.write_standard_file(prefix="multiplane_ophys", output_directory=OUTPUT_PATH)
diff --git a/examples/ophys_procedures.py b/examples/ophys_procedures.py
@@ -22,6 +22,8 @@
     WaterRestriction,
 )
 
+OUTPUT_PATH = "examples/"
+
 t = datetime.datetime(2022, 7, 12, 7, 00, 00)
 t2 = datetime.datetime(2022, 9, 23, 10, 22, 00)
 
@@ -164,4 +166,4 @@
 )
 serialized = p.model_dump_json()
 deserialized = Procedures.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="ophys")
+deserialized.write_standard_file(prefix="ophys", output_directory=OUTPUT_PATH)
diff --git a/examples/ophys_session.py b/examples/ophys_session.py
@@ -6,6 +6,8 @@
 
 from aind_data_schema.core.session import DetectorConfig, FiberConnectionConfig, LaserConfig, Session, Stream
 
+OUTPUT_PATH = "examples/"
+
 t = datetime(2022, 7, 12, 7, 00, 00, tzinfo=timezone.utc)
 
 s = Session(
@@ -60,4 +62,4 @@
 )
 serialized = s.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="ophys")
+deserialized.write_standard_file(prefix="ophys", output_directory=OUTPUT_PATH)
diff --git a/examples/procedures.py b/examples/procedures.py
@@ -13,6 +13,8 @@
     ViralMaterial,
 )
 
+OUTPUT_PATH = "examples/"
+
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 7, 12, 7, 00, 00, tzinfo=timezone.utc)
@@ -81,4 +83,4 @@
 )
 serialized = p.model_dump_json()
 deserialized = Procedures.model_validate_json(serialized)
-deserialized.write_standard_file()
+deserialized.write_standard_file(output_directory=OUTPUT_PATH)
diff --git a/examples/processing.py b/examples/processing.py
@@ -4,6 +4,8 @@
 
 from aind_data_schema.core.processing import AnalysisProcess, DataProcess, PipelineProcess, Processing, ProcessName
 
+OUTPUT_PATH = "examples/"
+
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 11, 22, 8, 43, 00, tzinfo=timezone.utc)
@@ -80,4 +82,4 @@
 )
 serialized = p.model_dump_json()
 deserialized = Processing.model_validate_json(serialized)
-p.write_standard_file()
+p.write_standard_file(output_directory=OUTPUT_PATH)
diff --git a/examples/subject.py b/examples/subject.py
@@ -7,6 +7,8 @@
 
 from aind_data_schema.core.subject import BreedingInfo, Housing, Sex, Subject
 
+OUTPUT_PATH = "examples/"
+
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 11, 22, 8, 43, 00, tzinfo=timezone.utc)
@@ -30,4 +32,4 @@
 )
 serialized = s.model_dump_json()
 deserialized = Subject.model_validate_json(serialized)
-deserialized.write_standard_file()
+deserialized.write_standard_file(output_directory=OUTPUT_PATH)
diff --git a/src/aind_data_schema/utils/examples_generator.py b/src/aind_data_schema/utils/examples_generator.py
@@ -0,0 +1,37 @@
+"""script for re-generating all examples"""
+
+import os
+import runpy
+from glob import glob
+from pathlib import Path
+import logging
+
+CURRENT_DIR = Path(os.path.dirname(os.path.realpath(__file__)))
+ROOT_DIR = CURRENT_DIR.parents[2]
+EXAMPLES_DIR = ROOT_DIR / "examples"
+
+
+class ExamplesGenerator:
+    """Class to generate example files from .py files in examples directory"""
+
+    def generate_all_examples(self):
+        """Generate all examples in EXAMPLES_DIR"""
+
+        logging.info(f"Running all examples in {EXAMPLES_DIR}")
+        for example_file in glob(f"{EXAMPLES_DIR}/*.py"):
+            logging.info(f"Running {example_file}")
+            runpy.run_path(path_name=example_file)
+
+    def generate_example(self, example_file):
+        """Generate example from example_file"""
+
+        logging.info(f"Running {example_file}")
+        try:
+            runpy.run_path(path_name=example_file)
+        except Exception as e:
+            logging.info(f"Error running {example_file}: {e}")
+
+
+if __name__ == "__main__":
+    """Run all examples in EXAMPLES_DIR"""
+    ExamplesGenerator().generate_all_examples()
diff --git a/tests/test_examples_generator.py b/tests/test_examples_generator.py
@@ -0,0 +1,28 @@
+"""Module to test the examples_generator.py script"""
+
+import unittest
+from unittest.mock import patch
+
+from aind_data_schema.utils.examples_generator import ExamplesGenerator
+
+
+class ExamplesGeneratorTest(unittest.TestCase):
+    """Tests for ExamplesGenerator methods"""
+
+    @patch("aind_data_schema.base.AindCoreModel.write_standard_file")
+    def test_generate_all_files(self, mocked_run_path):
+        """Test generate_all_examples method"""
+
+        ExamplesGenerator().generate_all_examples()
+
+    @patch("aind_data_schema.base.AindCoreModel.write_standard_file")
+    def test_generate_example(self, mocked_run_path):
+        """Test generate_example method"""
+
+        ExamplesGenerator().generate_example(
+            "C:/Users/mae.moninghoff/Documents/GitHub/aind-data-schema/examples/subject.py"
+        )
+
+        ExamplesGenerator().generate_example(
+            "fake/path/to/example.py"
+        )

Original file line number	Diff line number	Diff line change
`@@ -16,6 +16,8 @@`
`16`	`16`	`)`
`17`	`17`	`from aind_data_schema.core.instrument import Com, Instrument`
`18`	`18`
	`19`	`+OUTPUT_PATH = "examples/"`
	`20`	`+`
`19`	`21`	`inst = Instrument(`
`20`	`22`	`instrument_id="440_SmartSPIM2_20231004",`
`21`	`23`	`modification_date=datetime.date(2023, 10, 4),`
`@@ -211,4 +213,4 @@`
`211`	`213`	`)`
`212`	`214`	`serialized = inst.model_dump_json()`
`213`	`215`	`deserialized = Instrument.model_validate_json(serialized)`
`214`		`-deserialized.write_standard_file(prefix="aibs_smartspim")`
	`216`	`+deserialized.write_standard_file(prefix="aibs_smartspim", output_directory=OUTPUT_PATH)`
Original file line number	Diff line number	Diff line change
`@@ -28,6 +28,8 @@`
`28`	`28`	`)`
`29`	`29`	`from aind_data_schema.core.rig import Rig`
`30`	`30`
	`31`	`+OUTPUT_PATH = "examples/"`
	`32`	`+`
`31`	`33`	`# Describes a rig with running wheel, 2 behavior cameras, one Harp Behavior board,`
`32`	`34`	`# one dual-color laser module, one stick microscope, and 2 Neuropixels probes`
`33`	`35`
`@@ -213,4 +215,4 @@`
`213`	`215`	`)`
`214`	`216`	`serialized = rig.model_dump_json()`
`215`	`217`	`deserialized = Rig.model_validate_json(serialized)`
`216`		`-deserialized.write_standard_file(prefix="ephys")`
	`218`	`+deserialized.write_standard_file(prefix="ephys", output_directory=OUTPUT_PATH)`