diff --git a/.github/workflows/test_and_lint.yml b/.github/workflows/test_and_lint.yml index e2d22e9..7593130 100644 --- a/.github/workflows/test_and_lint.yml +++ b/.github/workflows/test_and_lint.yml @@ -4,13 +4,16 @@ on: pull_request: branches: - main + - dev jobs: ci: - runs-on: ubuntu-latest + runs-on: ${{ matrix.os }} strategy: + fail-fast: true matrix: - python-version: [ '3.10', '3.11', '3.12' ] + os: [ ubuntu-latest, macos-latest, windows-latest ] + python-version: [ '3.12' ] steps: - uses: actions/checkout@v6 - name: Set up Python ${{ matrix.python-version }} @@ -20,6 +23,6 @@ jobs: - name: Install dependencies run: uv sync - name: Run linter checks - run: uv run flake8 . && uv run interrogate --verbose . + run: uv run ruff check . && uv run ruff format --check . && uv run interrogate --verbose . - name: Run tests and coverage - run: uv run coverage run -m unittest discover && uv run coverage report + run: uv run coverage run -m pytest && uv run coverage report diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3c23d24..b8035bc 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,33 +2,43 @@ ### Linters and testing -There are several libraries used to run linters, check documentation, and run tests. +This project uses [uv](https://docs.astral.sh/uv/) to manage its environment and +[ruff](https://docs.astral.sh/ruff/) for linting and formatting. -- Please test your changes using the **coverage** library, which will run the tests and log a coverage report: +- Install dependencies (including the `dev` group): ```bash -coverage run -m unittest discover && coverage report +uv sync +``` + +- Run tests with **pytest** under **coverage**: + +```bash +uv run coverage run -m pytest && uv run coverage report ``` - Use **interrogate** to check that modules, methods, etc. have been documented thoroughly: ```bash -interrogate . +uv run interrogate . ``` -- Use **flake8** to check that code is up to standards (no unused imports, etc.): +- Use **ruff** to lint the code (catches unused imports, style issues, sorts imports, etc.): + ```bash -flake8 . +uv run ruff check . ``` -- Use **black** to automatically format the code into PEP standards: +- Use **ruff** to automatically format the code: + ```bash -black . +uv run ruff format . ``` -- Use **isort** to automatically sort import statements: +- To apply ruff's autofixes in one shot: + ```bash -isort . +uv run ruff check --fix . && uv run ruff format . ``` ### Pull requests diff --git a/examples/raw_data_loader_example.ipynb b/examples/raw_data_loader_example.ipynb new file mode 100644 index 0000000..251b20c --- /dev/null +++ b/examples/raw_data_loader_example.ipynb @@ -0,0 +1,368 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "7706de71", + "metadata": {}, + "source": [ + "# RawDataLoader Example\n", + "\n", + "This notebook demonstrates how to use `RawDataLoader` from `dynamic_foraging_processing` to load raw dynamic foraging data via the `aind-behavior-dynamic-foraging` data contract.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "46cbc8b3", + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2\n", + "from pathlib import Path\n", + "\n", + "from dynamic_foraging_processing.raw_data_loader import RawDataLoader" + ] + }, + { + "cell_type": "markdown", + "id": "5125cc85", + "metadata": {}, + "source": [ + "## Create a loader\n", + "\n", + "Point `RawDataLoader` at the root directory of a dataset acquisition.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "628b1d61", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Update this path to point at a real acquisition directory on your machine.\n", + "dataset_path = Path(r\"C:\\Users\\arjun.sridhar\\Downloads\\821586_2026-04-28T200347Z\\821586_2026-04-28T200347Z\")\n", + "\n", + "loader = RawDataLoader(path=dataset_path)\n", + "loader" + ] + }, + { + "cell_type": "markdown", + "id": "18bce795", + "metadata": {}, + "source": [ + "## Access an individual stream\n", + "\n", + "You can load a single stream directly from `loader.dataset` without loading every stream in the dataset. See the [data contract]( https://github.com/AllenNeuralDynamics/Aind.Behavior.DynamicForaging/blob/main/src/aind_behavior_dynamic_foraging/data_contract/_dataset.py) on how to access the various streams via the tree-like contract. An example is shown below\n" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "64ba5e4b", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'foraging_efficiency_per_session': [1.4866204162537167],\n", + " 'unignored_trials_per_session': [527],\n", + " 'total_sessions': 1,\n", + " 'consecutive_sessions_at_current_stage': 1,\n", + " 'stage_name': 'stage_2'}" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "stream = loader.dataset.at(\"Behavior\").at(\"PreviousMetrics\").load().data\n", + "stream" + ] + }, + { + "cell_type": "markdown", + "id": "73ad95a1", + "metadata": {}, + "source": [ + "## Load all raw data\n", + "\n", + "`get_all_raw_data` returns a dictionary mapping each stream to its loaded data (a `pandas.DataFrame` or a `dictionary`). Note that the keys returned chain the parent stream and the current stream, since some child leaf node streams have the same name but come from different parents. This dictionary here will then be used to create the acquisition container in the NWB file\n" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "25e14aae", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Deserialized versioned field 0.13.5, expected 0.13.7. Will attempt to coerce. This will be considered a best-effort operation.\n", + "Deserialized versioned field 0.13.5, expected 0.13.7. Will attempt to coerce. This will be considered a best-effort operation.\n", + "Deserialized versioned field 0.13.5, expected 0.13.7. Will attempt to coerce. This will be considered a best-effort operation.\n", + "Deserialized versioned field 0.13.5, expected 0.13.7. Will attempt to coerce. This will be considered a best-effort operation.\n" + ] + }, + { + "data": { + "text/plain": [ + "['Behavior.PreviousMetrics',\n", + " 'Behavior.TrainerState',\n", + " 'HarpBehavior.WhoAmI',\n", + " 'HarpBehavior.HardwareVersionHigh',\n", + " 'HarpBehavior.HardwareVersionLow',\n", + " 'HarpBehavior.AssemblyVersion',\n", + " 'HarpBehavior.CoreVersionHigh',\n", + " 'HarpBehavior.CoreVersionLow',\n", + " 'HarpBehavior.FirmwareVersionHigh',\n", + " 'HarpBehavior.FirmwareVersionLow',\n", + " 'HarpBehavior.TimestampSeconds',\n", + " 'HarpBehavior.TimestampMicroseconds',\n", + " 'HarpBehavior.OperationControl',\n", + " 'HarpBehavior.ResetDevice',\n", + " 'HarpBehavior.DeviceName',\n", + " 'HarpBehavior.SerialNumber',\n", + " 'HarpBehavior.ClockConfiguration',\n", + " 'HarpBehavior.DigitalInputState',\n", + " 'HarpBehavior.OutputSet',\n", + " 'HarpBehavior.OutputClear',\n", + " 'HarpBehavior.OutputToggle',\n", + " 'HarpBehavior.OutputState',\n", + " 'HarpBehavior.PortDIOSet',\n", + " 'HarpBehavior.PortDIOClear',\n", + " 'HarpBehavior.PortDIOToggle',\n", + " 'HarpBehavior.PortDIOState',\n", + " 'HarpBehavior.PortDIODirection',\n", + " 'HarpBehavior.PortDIOStateEvent',\n", + " 'HarpBehavior.AnalogData',\n", + " 'HarpBehavior.OutputPulseEnable',\n", + " 'HarpBehavior.PulseDOPort0',\n", + " 'HarpBehavior.PulseDOPort1',\n", + " 'HarpBehavior.PulseDOPort2',\n", + " 'HarpBehavior.PulseSupplyPort0',\n", + " 'HarpBehavior.PulseSupplyPort1',\n", + " 'HarpBehavior.PulseSupplyPort2',\n", + " 'HarpBehavior.PulseLed0',\n", + " 'HarpBehavior.PulseLed1',\n", + " 'HarpBehavior.PulseRgb0',\n", + " 'HarpBehavior.PulseRgb1',\n", + " 'HarpBehavior.PulseDO0',\n", + " 'HarpBehavior.PulseDO1',\n", + " 'HarpBehavior.PulseDO2',\n", + " 'HarpBehavior.PulseDO3',\n", + " 'HarpBehavior.PwmFrequencyDO0',\n", + " 'HarpBehavior.PwmFrequencyDO1',\n", + " 'HarpBehavior.PwmFrequencyDO2',\n", + " 'HarpBehavior.PwmFrequencyDO3',\n", + " 'HarpBehavior.PwmDutyCycleDO0',\n", + " 'HarpBehavior.PwmDutyCycleDO1',\n", + " 'HarpBehavior.PwmDutyCycleDO2',\n", + " 'HarpBehavior.PwmDutyCycleDO3',\n", + " 'HarpBehavior.PwmStart',\n", + " 'HarpBehavior.PwmStop',\n", + " 'HarpBehavior.RgbAll',\n", + " 'HarpBehavior.Rgb0',\n", + " 'HarpBehavior.Rgb1',\n", + " 'HarpBehavior.Led0Current',\n", + " 'HarpBehavior.Led1Current',\n", + " 'HarpBehavior.Led0MaxCurrent',\n", + " 'HarpBehavior.Led1MaxCurrent',\n", + " 'HarpBehavior.EventEnable',\n", + " 'HarpBehavior.StartCameras',\n", + " 'HarpBehavior.StopCameras',\n", + " 'HarpBehavior.EnableServos',\n", + " 'HarpBehavior.DisableServos',\n", + " 'HarpBehavior.EnableEncoders',\n", + " 'HarpBehavior.EncoderMode',\n", + " 'HarpBehavior.Camera0Frame',\n", + " 'HarpBehavior.Camera0Frequency',\n", + " 'HarpBehavior.Camera1Frame',\n", + " 'HarpBehavior.Camera1Frequency',\n", + " 'HarpBehavior.ServoMotor2Period',\n", + " 'HarpBehavior.ServoMotor2Pulse',\n", + " 'HarpBehavior.ServoMotor3Period',\n", + " 'HarpBehavior.ServoMotor3Pulse',\n", + " 'HarpBehavior.EncoderReset',\n", + " 'HarpBehavior.EnableSerialTimestamp',\n", + " 'HarpBehavior.MimicPort0IR',\n", + " 'HarpBehavior.MimicPort1IR',\n", + " 'HarpBehavior.MimicPort2IR',\n", + " 'HarpBehavior.MimicPort0Valve',\n", + " 'HarpBehavior.MimicPort1Valve',\n", + " 'HarpBehavior.MimicPort2Valve',\n", + " 'HarpBehavior.PokeInputFilter',\n", + " 'InputSchemas.Rig',\n", + " 'InputSchemas.TaskLogic',\n", + " 'InputSchemas.Session']" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "raw_data = loader.get_all_raw_data()\n", + "list(raw_data.keys())" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "080d09b6", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Looking at stream Behavior.PreviousMetrics:\n" + ] + }, + { + "data": { + "text/plain": [ + "{'foraging_efficiency_per_session': [1.4866204162537167],\n", + " 'unignored_trials_per_session': [527],\n", + " 'total_sessions': 1,\n", + " 'consecutive_sessions_at_current_stage': 1,\n", + " 'stage_name': 'stage_2'}" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Inspect same stream from fully loaded raw data\n", + "stream_name = next(iter(raw_data))\n", + "print(f\"Looking at stream {stream_name}:\")\n", + "raw_data[stream_name]" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "87d922f2", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Looking at stream InputSchemas.TaskLogic:\n" + ] + }, + { + "data": { + "text/plain": [ + "{'name': 'AindDynamicForaging',\n", + " 'description': '',\n", + " 'task_parameters': {'rng_seed': None,\n", + " 'aind_behavior_services_pkg_version': '0.13.7',\n", + " 'reward_size': {'right_value_volume': 2.0, 'left_value_volume': 2.0},\n", + " 'trial_generator': {'type': 'CoupledTrialGenerator',\n", + " 'quiescent_duration': {'family': ,\n", + " 'distribution_parameters': {'family': ,\n", + " 'value': 0.0},\n", + " 'truncation_parameters': None,\n", + " 'scaling_parameters': None},\n", + " 'response_duration': 3.0,\n", + " 'reward_consumption_duration': 1.0,\n", + " 'inter_trial_interval_duration': {'family': ,\n", + " 'distribution_parameters': {'family': ,\n", + " 'rate': 0.2},\n", + " 'truncation_parameters': {'truncation_mode': 'exclude',\n", + " 'min': 1.0,\n", + " 'max': 10.0},\n", + " 'scaling_parameters': None},\n", + " 'block_len': {'family': ,\n", + " 'distribution_parameters': {'family': ,\n", + " 'rate': 0.05},\n", + " 'truncation_parameters': {'truncation_mode': 'exclude',\n", + " 'min': 20.0,\n", + " 'max': 60.0},\n", + " 'scaling_parameters': None},\n", + " 'min_block_reward': 0,\n", + " 'kernel_size': 2,\n", + " 'reward_probability_parameters': {'base_reward_sum': 0.6,\n", + " 'reward_pairs': [[8.0, 1.0]]},\n", + " 'autowater_parameters': {'min_ignored_trials': 7,\n", + " 'min_unrewarded_trials': 7,\n", + " 'reward_fraction': 0.5},\n", + " 'is_baiting': False,\n", + " 'trial_generation_end_parameters': {'ignore_win': 30,\n", + " 'ignore_ratio_threshold': 0.83,\n", + " 'max_trial': 1000,\n", + " 'max_time': 4500.0,\n", + " 'min_time': 1800.0},\n", + " 'behavior_stability_parameters': {'behavior_evaluation_mode': 'end',\n", + " 'behavior_stability_fraction': 0.6,\n", + " 'min_consecutive_stable_trials': 5},\n", + " 'extend_block_on_no_response': True}},\n", + " 'version': '0.0.2-rc27',\n", + " 'stage_name': None}" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Inspect another stream\n", + "stream_name = \"InputSchemas.TaskLogic\"\n", + "print(f\"Looking at stream {stream_name}:\")\n", + "raw_data[stream_name].model_dump()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dd1a8aa9", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "dynamic-foraging-processing", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pyproject.toml b/pyproject.toml index 02b10b9..687ac1e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" name = "dynamic-foraging-processing" description = "Generated from aind-library-template" license = "MIT" -requires-python = ">=3.10" +requires-python = ">=3.12" authors = [ {name = "Allen Institute for Neural Dynamics"} ] @@ -17,15 +17,16 @@ readme = "README.md" version = "0.0.0" dependencies = [ + "aind-behavior-dynamic-foraging[data] @ git+https://github.com/AllenNeuralDynamics/Aind.Behavior.DynamicForaging.git@v0.0.2rc27", + "ipykernel", ] [dependency-groups] dev = [ - 'black', + 'ruff', 'coverage', - 'flake8', 'interrogate', - 'isort', + 'pytest', 'Sphinx', 'furo' ] @@ -33,30 +34,25 @@ dev = [ [tool.setuptools.packages.find] where = ["src"] -[tool.black] -line-length = 79 -target_version = ['py310'] -exclude = ''' +[tool.ruff] +line-length = 120 +target-version = 'py312' +extend-exclude = [ + '.conda', + '.venv', + 'build', + 'dist', +] + +[tool.ruff.lint] +extend-select = ['Q', 'RUF100', 'C90', 'I'] +extend-ignore = [] -( - /( - \.eggs # exclude a few common directories in the - | \.git # root of the project - | \.hg - | \.mypy_cache - | \.tox - | \.venv - | _build - | build - | dist - | .conda - )/ - | .gitignore -) -''' +[tool.ruff.lint.pydocstyle] +convention = 'google' [tool.coverage.run] -omit = ["*__init__*"] +omit = ["*__init__*", "*/temp_dataset.py"] source = ["dynamic_foraging_processing", "tests"] [tool.coverage.report] @@ -64,15 +60,12 @@ exclude_lines = [ "if __name__ == .__main__.:", "^from .* import .*", "^import .*", + "if t\\.TYPE_CHECKING:", + "if TYPE_CHECKING:", "pragma: no cover" ] fail_under = 100 -[tool.isort] -line_length = 79 -profile = "black" -skip = [".conda", ".venv"] - [tool.interrogate] exclude = ["setup.py", "docs", "build", ".conda"] fail-under = 100 diff --git a/src/dynamic_foraging_processing/raw_data_loader/__init__.py b/src/dynamic_foraging_processing/raw_data_loader/__init__.py new file mode 100644 index 0000000..13c6a0a --- /dev/null +++ b/src/dynamic_foraging_processing/raw_data_loader/__init__.py @@ -0,0 +1,5 @@ +"""Raw data loader package.""" + +from .raw_data_loader import RawDataLoader + +__all__ = ["RawDataLoader"] diff --git a/src/dynamic_foraging_processing/raw_data_loader/raw_data_loader.py b/src/dynamic_foraging_processing/raw_data_loader/raw_data_loader.py new file mode 100644 index 0000000..fd6138c --- /dev/null +++ b/src/dynamic_foraging_processing/raw_data_loader/raw_data_loader.py @@ -0,0 +1,88 @@ +"""Raw data loader for dynamic foraging datasets.""" + +import logging +import os +import typing as t + +import pandas as pd + +from .temp_dataset import dataset as _build_dataset + +if t.TYPE_CHECKING: + from contraqctor.contract import Dataset + +logger = logging.getLogger(__name__) + + +class RawDataLoader: + """Loads raw dynamic foraging data using the aind-behavior-dynamic-foraging data contract.""" + + def __init__( + self, + path: os.PathLike, + dataset: t.Optional["Dataset"] = None, + raise_on_error: bool = False, + ): + """Initialize the raw data loader. + + Parameters + ---------- + path : os.PathLike + Path to the dataset root directory. + dataset : Dataset, optional + Pre-built ``Dataset`` object. If ``None``, a ``Dataset`` is + instantiated at the latest version using the data contract. + raise_on_error : bool, optional + If ``True``, raise on errors encountered while loading data. + Defaults to ``False``. + """ + if dataset is None: + dataset = _build_dataset(path) + self.path = path + self.dataset = dataset + self.raise_on_error = raise_on_error + + def get_all_raw_data(self) -> t.Dict[str, t.Union[pd.DataFrame, t.Dict]]: + """Raw data loaded from ``self.dataset``. + + Returns + ------- + dict of str to pandas.DataFrame or dict + Mapping of stream name to the stream's loaded data. + """ + streams = self.dataset.load_all() + raw_data_dict: t.Dict[str, t.Union[pd.DataFrame, t.Dict]] = {} + for stream in streams.iter_all(): + if stream.is_collection: # only process leaf nodes for data + err = stream.collect_errors() + if err: + logger.debug(f"Collection stream {stream.name} has errors: {err}") + if self.raise_on_error: + raise ValueError(f"Collection stream {stream.name} has errors: {err}") + continue + + if stream.has_error: + logger.debug(f"Stream {stream.name} has error: {stream.collect_errors()}") + if self.raise_on_error: + raise ValueError(f"Stream {stream.name} has error: {stream.collect_errors()}") + + raw_data_dict[stream.name] = ( + f"No data. Failed to load stream {stream.name} with error: {stream.collect_errors()}" + ) + + raw_data_dict[f"{stream.parent.name}.{stream.name}"] = stream.data + logger.debug(f"Stream {stream.name} loaded successfully.") + + return raw_data_dict + + @property + def raw_data_metadata(self) -> t.Dict[str, str]: + """Descriptions for each stream in ``self.dataset`` + Will mainly be used for NWB. + + Returns + ------- + dict of str to str + Mapping of stream name to the stream's description. + """ + return {f"{stream.parent.name}.{stream.name}": stream.description for stream in self.dataset.iter_all()} diff --git a/src/dynamic_foraging_processing/raw_data_loader/temp_dataset.py b/src/dynamic_foraging_processing/raw_data_loader/temp_dataset.py new file mode 100644 index 0000000..561f477 --- /dev/null +++ b/src/dynamic_foraging_processing/raw_data_loader/temp_dataset.py @@ -0,0 +1,117 @@ +"""Temporary local dataset builder. + +This is a local copy of ``aind_behavior_dynamic_foraging.data_contract._dataset.make_dataset``. +This file ONLY exists because test data has only been acquired. +It will be removed once the full dataset is acquired. +""" + +from pathlib import Path + +from aind_behavior_curriculum import TrainerState +from aind_behavior_dynamic_foraging import __semver__ +from aind_behavior_dynamic_foraging.rig import AindDynamicForagingRig +from aind_behavior_dynamic_foraging.task_logic import AindDynamicForagingTaskLogic +from aind_behavior_services.session import Session +from contraqctor.contract import Dataset, DataStreamCollection +from contraqctor.contract.harp import ( + DeviceYmlByFile, + HarpDevice, +) +from contraqctor.contract.json import Json, PydanticModel + + +def make_dataset( + root_path: Path, + name: str = "DynamicForagingDataset", + description: str = "A Dynamic Foraging dataset", + version: str = __semver__, +) -> Dataset: + """Creates a Dataset object for the Dynamic Foraging experiment. + + This function constructs a hierarchical representation of the data streams + collected during an experiment, including hardware device data, software + events, and configuration files. + + Parameters + ---------- + root_path : Path + Path to the root directory containing the dataset. + name : str, optional + Name of the dataset, defaults to ``"DynamicForagingDataset"``. + description : str, optional + Description of the dataset, defaults to ``"A Dynamic Foraging dataset"``. + version : str, optional + Version of the dataset, defaults to the package version. + + Returns + ------- + Dataset + A Dataset object containing a hierarchical representation of all data + streams from the Dynamic Foraging experiment. + """ + root_path = Path(root_path) + return Dataset( + name=name, + version=version, + description=description, + data_streams=[ + DataStreamCollection( + name="Behavior", + description="Data from the Behavior modality", + data_streams=[ + Json( + name="PreviousMetrics", + reader_params=Json.make_params( + path=root_path / "behavior/metrics.json", + ), + ), + PydanticModel( + name="TrainerState", + reader_params=PydanticModel.make_params( + model=TrainerState, + path=root_path / "behavior/trainer_state.json", + ), + ), + HarpDevice( + name="HarpBehavior", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/Behavior.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + DataStreamCollection( + name="InputSchemas", + description="Configuration files for the behavior rig, task_logic and session.", + data_streams=[ + PydanticModel( + name="Rig", + reader_params=PydanticModel.make_params( + model=AindDynamicForagingRig, + path=root_path / "behavior/Logs/rig_output.json", + ), + ), + PydanticModel( + name="TaskLogic", + reader_params=PydanticModel.make_params( + model=AindDynamicForagingTaskLogic, + path=root_path / "behavior/Logs/tasklogic_output.json", + ), + ), + PydanticModel( + name="Session", + reader_params=PydanticModel.make_params( + model=Session, + path=root_path / "behavior/Logs/session_output.json", + ), + ), + ], + ), + ], + ), + ], + ) + + +def dataset(path, version: str = __semver__) -> Dataset: + """Build a Dataset at ``path`` using the local (temp) make_dataset.""" + return make_dataset(Path(path), version=version) diff --git a/tests/test_raw_data_loader/__init__.py b/tests/test_raw_data_loader/__init__.py new file mode 100644 index 0000000..02b98bf --- /dev/null +++ b/tests/test_raw_data_loader/__init__.py @@ -0,0 +1 @@ +"""Tests for the ``raw_data_loader`` package.""" diff --git a/tests/test_raw_data_loader/test_raw_data_loader.py b/tests/test_raw_data_loader/test_raw_data_loader.py new file mode 100644 index 0000000..13591e3 --- /dev/null +++ b/tests/test_raw_data_loader/test_raw_data_loader.py @@ -0,0 +1,139 @@ +"""Tests for ``dynamic_foraging_processing.raw_data_loader.raw_data_loader``.""" + +from unittest.mock import MagicMock, patch + +import pytest + +from dynamic_foraging_processing.raw_data_loader import RawDataLoader + + +def _make_stream( + name, + parent_name="Parent", + is_collection=False, + has_error=False, + errors=None, + data="data", + description="desc", +): + """Build a mock stream with the attributes accessed by ``RawDataLoader``.""" + stream = MagicMock() + stream.name = name + stream.parent.name = parent_name + stream.is_collection = is_collection + stream.has_error = has_error + stream.collect_errors.return_value = errors + stream.data = data + stream.description = description + return stream + + +def _make_dataset(streams_for_load_all=None, streams_for_iter_all=None): + """Build a mock dataset whose ``load_all`` and ``iter_all`` return the given streams.""" + dataset = MagicMock() + loaded = MagicMock() + loaded.iter_all.return_value = list(streams_for_load_all or []) + dataset.load_all.return_value = loaded + dataset.iter_all.return_value = list(streams_for_iter_all or []) + return dataset + + +# --------------------------------------------------------------------------- +# __init__ +# --------------------------------------------------------------------------- + + +def test_init_with_dataset(): + """Provided dataset is stored and ``_build_dataset`` is not called.""" + ds = _make_dataset() + loader = RawDataLoader(path="some/path", dataset=ds) + assert loader.dataset is ds + assert loader.path == "some/path" + assert loader.raise_on_error is False + + +def test_init_without_dataset_builds(): + """When dataset is ``None`` the temp builder is invoked.""" + built = _make_dataset() + with patch( + "dynamic_foraging_processing.raw_data_loader.raw_data_loader._build_dataset", + return_value=built, + ) as build_mock: + loader = RawDataLoader(path="root") + build_mock.assert_called_once_with("root") + assert loader.dataset is built + assert loader.raise_on_error is False + + +def test_init_raise_on_error_true(): + """``raise_on_error`` flag is stored on the instance.""" + loader = RawDataLoader(path="p", dataset=_make_dataset(), raise_on_error=True) + assert loader.raise_on_error is True + + +# --------------------------------------------------------------------------- +# get_all_raw_data +# --------------------------------------------------------------------------- + + +def test_get_all_raw_data_collection_without_errors_is_skipped(): + """Collection streams without errors are skipped; leaves are collected.""" + collection = _make_stream("Col", is_collection=True, errors=None) + leaf = _make_stream("Leaf", parent_name="Col", data="payload") + ds = _make_dataset(streams_for_load_all=[collection, leaf]) + loader = RawDataLoader(path="p", dataset=ds) + assert loader.get_all_raw_data() == {"Col.Leaf": "payload"} + + +def test_get_all_raw_data_collection_with_errors_no_raise(): + """Collection errors are logged and skipped when ``raise_on_error`` is False.""" + collection = _make_stream("Col", is_collection=True, errors=["boom"]) + ds = _make_dataset(streams_for_load_all=[collection]) + loader = RawDataLoader(path="p", dataset=ds, raise_on_error=False) + assert loader.get_all_raw_data() == {} + + +def test_get_all_raw_data_collection_with_errors_raise(): + """Collection errors raise when ``raise_on_error`` is True.""" + collection = _make_stream("Col", is_collection=True, errors=["boom"]) + ds = _make_dataset(streams_for_load_all=[collection]) + loader = RawDataLoader(path="p", dataset=ds, raise_on_error=True) + with pytest.raises(ValueError): + loader.get_all_raw_data() + + +def test_get_all_raw_data_leaf_has_error_no_raise(): + """Leaf errors are tolerated when ``raise_on_error`` is False.""" + leaf = _make_stream( + "Leaf", + parent_name="Col", + has_error=True, + errors=["bad"], + data="payload", + ) + ds = _make_dataset(streams_for_load_all=[leaf]) + loader = RawDataLoader(path="p", dataset=ds, raise_on_error=False) + assert "Col.Leaf" in loader.get_all_raw_data() + + +def test_get_all_raw_data_leaf_has_error_raise(): + """Leaf errors raise when ``raise_on_error`` is True.""" + leaf = _make_stream("Leaf", parent_name="Col", has_error=True, errors=["bad"]) + ds = _make_dataset(streams_for_load_all=[leaf]) + loader = RawDataLoader(path="p", dataset=ds, raise_on_error=True) + with pytest.raises(ValueError): + loader.get_all_raw_data() + + +# --------------------------------------------------------------------------- +# raw_data_metadata +# --------------------------------------------------------------------------- + + +def test_raw_data_metadata(): + """Maps ``parent.name`` to each stream description.""" + s1 = _make_stream("A", parent_name="P", description="d1") + s2 = _make_stream("B", parent_name="P", description="d2") + ds = _make_dataset(streams_for_iter_all=[s1, s2]) + loader = RawDataLoader(path="p", dataset=ds) + assert loader.raw_data_metadata == {"P.A": "d1", "P.B": "d2"} diff --git a/uv.lock b/uv.lock index fae093d..0defb37 100644 --- a/uv.lock 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