diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000..dac1e04 --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,59 @@ +name: Tests + +on: + push: + branches: [main] + pull_request: + +jobs: + test: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ['3.10', '3.11', '3.12'] + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + cache: 'pip' + cache-dependency-path: | + processor/requirements.txt + requirements-test.txt + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r processor/requirements.txt + pip install -r requirements-test.txt + + - name: Run tests with coverage + run: | + python -m pytest tests/ -v --cov=processor --cov-report=xml --cov-report=term-missing + + lint: + runs-on: ubuntu-latest + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.12' + cache: 'pip' + + - name: Install linting tools + run: | + python -m pip install --upgrade pip + pip install ruff + + - name: Run linter + run: | + ruff check processor/ tests/ --output-format=github + continue-on-error: true diff --git a/.gitignore b/.gitignore index 4f2d0fe..7962c07 100644 --- a/.gitignore +++ b/.gitignore @@ -49,6 +49,9 @@ coverage.xml .pytest_cache/ cover/ +# Virtualenv +venv/ + # Swap [._]*.s[a-v][a-z] [._]*.sw[a-p] diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..5c51302 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,7 @@ +repos: + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.8.3 + hooks: + - id: ruff + args: [--fix, --exit-non-zero-on-fix] + - id: ruff-format diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/Makefile b/Makefile index 8d58257..fb38c71 100644 --- a/Makefile +++ b/Makefile @@ -1,14 +1,49 @@ -.PHONY: help test run +.PHONY: help run clean venv install test test-cov lint pre-commit SERVICE_NAME ?= "processor-post-timeseries" +VENV_DIR ?= venv +PYTHON ?= python3 .DEFAULT: help help: @echo "Make Help for $(SERVICE_NAME)" @echo "" - @echo "make run - run the processor locally via docker-compose" - @echo "make clean - remove all files from locally mounted input / output directories" + @echo "make venv - create virtual environment and install all dependencies" + @echo "make install - install dependencies into existing venv" + @echo "make pre-commit - install pre-commit hooks" + @echo "make test - run tests" + @echo "make test-cov - run tests with coverage report" + @echo "make lint - run linter with auto-fix" + @echo "make run - run the processor locally via docker-compose" + @echo "make clean - remove all files from locally mounted input / output directories" + +venv: + $(PYTHON) -m venv $(VENV_DIR) + $(VENV_DIR)/bin/pip install --upgrade pip + $(VENV_DIR)/bin/pip install -r processor/requirements.txt + $(VENV_DIR)/bin/pip install -r requirements-test.txt + @echo "" + @echo "Virtual environment created. Activate with:" + @echo " source $(VENV_DIR)/bin/activate" + +install: + $(VENV_DIR)/bin/pip install --upgrade pip + $(VENV_DIR)/bin/pip install -r processor/requirements.txt + $(VENV_DIR)/bin/pip install -r requirements-test.txt + +test: + $(VENV_DIR)/bin/python -m pytest tests/ -v + +test-cov: + $(VENV_DIR)/bin/python -m pytest tests/ -v --cov=processor --cov-report=term-missing + +lint: + $(VENV_DIR)/bin/ruff check --fix processor/ tests/ + $(VENV_DIR)/bin/ruff format processor/ tests/ + +pre-commit: + $(VENV_DIR)/bin/pre-commit install run: docker-compose -f docker-compose.yml down --remove-orphans diff --git a/README.md b/README.md index 81aa241..c5dc22e 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,157 @@ # processor-post-timeseries -Timeseries Ingest Post Processor + +A processor for converting NWB (Neurodata Without Borders) files into chunked +timeseries data for the Pennsieve platform. + +## Overview + +This processor reads electrical series data from NWB files and: +1. Extracts channel data with proper scaling (conversion factors, offsets) +2. Writes chunked binary files (gzip-compressed, big-endian float64) +3. Generates channel metadata files (JSON) +4. Optionally uploads the processed data to Pennsieve via the import API + +## Architecture + +**main.py** - Entry point that orchestrates the processing pipeline. + +**reader.py** - `NWBElectricalSeriesReader` reads NWB ElectricalSeries data, +handles timestamps and sampling rates, applies conversion factors and offsets, +and detects contiguous data chunks. + +**writer.py** - `TimeSeriesChunkWriter` writes chunked binary data (.bin.gz) +and channel metadata (.metadata.json) in big-endian format. + +**importer.py** - Creates import manifests via Pennsieve API +and uploads files to S3 via presigned URLs. + +**clients/** - API clients for Pennsieve: +- `AuthenticationClient` - AWS Cognito authentication +- `ImportClient` - Import manifest creation and file upload +- `TimeSeriesClient` - Time series channel management +- `WorkflowClient` - Analytic workflow instance management +- `BaseClient` - Session management with auto-refresh + +## Setup + +### Prerequisites + +- Python 3.10+ +- Docker (for local runs) + +### Create Virtual Environment + +```bash +make venv +source venv/bin/activate +``` + +### Install Dependencies + +```bash +make install +``` + +## Development + +### Install Pre-commit Hooks + +This installs git hooks that automatically lint and format code on commit. + +```bash +make pre-commit +``` + +### Run Tests + +```bash +make test +``` + +### Run Tests with Coverage + +```bash +make test-cov +``` + +### Run Linter + +Runs ruff with auto-fix and formatting. + +```bash +make lint +``` + +## Running Locally + +### 1. Configure Environment + +Configure the environment file + +Edit `dev.env` with your settings: + +```env +ENVIRONMENT=local +INPUT_DIR=/data/input +OUTPUT_DIR=/data/output +CHUNK_SIZE_MB=1 +IMPORTER_ENABLED=false +... +``` + +### 2. Add Input File + +Place your `.nwb` file in the `data/input/` directory: + +```bash +cp /path/to/your/file.nwb data/input/ +``` + +### 3. Run the Processor + +```bash +make run +``` + +This builds and runs the processor via Docker. +Output files will be written to `data/output/`. + +### 4. Clean Up + +Remove input/output files: + +```bash +make clean +``` + +## Output Format + +The processor generates two types of files per channel: + +### Binary Data Files +- Pattern: `channel-{index}_{start_us}_{end_us}.bin.gz` +- Format: Gzip-compressed big-endian float64 values +- Example: `channel-00001_1000000_2000000.bin.gz` + +### Metadata Files +- Pattern: `channel-{index}.metadata.json` +- Contains: name, rate, start, end, unit, type, group, properties + +## Environment Variables + +| Variable | Description | Default | +|----------|-------------|---------| +| `ENVIRONMENT` | Runtime environment (`local` or `production`) | `local` | +| `INPUT_DIR` | Directory containing NWB files | - | +| `OUTPUT_DIR` | Directory for output files | - | +| `CHUNK_SIZE_MB` | Size of each data chunk in MB | `1` | +| `IMPORTER_ENABLED` | Enable Pennsieve upload | `false` | +| `PENNSIEVE_API_KEY` | Pennsieve API key | - | +| `PENNSIEVE_API_SECRET` | Pennsieve API secret | - | +| `PENNSIEVE_API_HOST` | Pennsieve API endpoint | `https://api.pennsieve.net` | +| `PENNSIEVE_API_HOST2` | Pennsieve API2 endpoint | `https://api2.pennsieve.net` | +| `INTEGRATION_ID` | Workflow instance ID | - | + +## License + +See LICENSE file. diff --git a/processor/clients/__init__.py b/processor/clients/__init__.py index 55543b7..f56b939 100644 --- a/processor/clients/__init__.py +++ b/processor/clients/__init__.py @@ -1,5 +1,8 @@ -from .base_client import SessionManager, BaseClient -from .authentication_client import AuthenticationClient -from .import_client import ImportClient, ImportFile -from .timeseries_client import TimeSeriesClient -from .workflow_client import WorkflowClient, WorkflowInstance +from .authentication_client import AuthenticationClient as AuthenticationClient +from .base_client import BaseClient as BaseClient +from .base_client import SessionManager as SessionManager +from .import_client import ImportClient as ImportClient +from .import_client import ImportFile as ImportFile +from .timeseries_client import TimeSeriesClient as TimeSeriesClient +from .workflow_client import WorkflowClient as WorkflowClient +from .workflow_client import WorkflowInstance as WorkflowInstance diff --git a/processor/clients/authentication_client.py b/processor/clients/authentication_client.py index a405d15..8cb9fc2 100644 --- a/processor/clients/authentication_client.py +++ b/processor/clients/authentication_client.py @@ -1,10 +1,12 @@ -import boto3 -import requests import json import logging +import boto3 +import requests + log = logging.getLogger() + class AuthenticationClient: def __init__(self, api_host): self.api_host = api_host @@ -28,9 +30,9 @@ def authenticate(self, api_key, api_secret): ) login_response = cognito_idp_client.initiate_auth( - AuthFlow="USER_PASSWORD_AUTH", - AuthParameters={"USERNAME": api_key, "PASSWORD": api_secret}, - ClientId=cognito_app_client_id, + AuthFlow="USER_PASSWORD_AUTH", + AuthParameters={"USERNAME": api_key, "PASSWORD": api_secret}, + ClientId=cognito_app_client_id, ) access_token = login_response["AuthenticationResult"]["AccessToken"] diff --git a/processor/clients/base_client.py b/processor/clients/base_client.py index 96d7079..5d224db 100644 --- a/processor/clients/base_client.py +++ b/processor/clients/base_client.py @@ -1,8 +1,10 @@ -import requests import logging +import requests + log = logging.getLogger() + # encapsulates a shared API session and re-authentication functionality class SessionManager: def __init__(self, authentication_client, api_key, api_secret): @@ -22,6 +24,7 @@ def session_token(self): def refresh_session(self): self.__session_token = self.authentication_client.authenticate(self.api_key, self.api_secret) + class BaseClient: def __init__(self, session_manager): self.session_manager = session_manager @@ -36,4 +39,5 @@ def wrapper(self, *args, **kwargs): self.session_manager.refresh_session() return func(self, *args, **kwargs) raise + return wrapper diff --git a/processor/clients/import_client.py b/processor/clients/import_client.py index 8d0856b..cad1874 100644 --- a/processor/clients/import_client.py +++ b/processor/clients/import_client.py @@ -1,22 +1,27 @@ -import requests import json import logging import math +import requests + from .base_client import BaseClient log = logging.getLogger() -MAX_REQUEST_SIZE_BYTES = 10 * 1024 * 1024 # AWS API Gateway payload limit of 10MB +MAX_REQUEST_SIZE_BYTES = 1 * 1024 * 1024 # AWS API Gateway payload limit of 10MB +DEFAULT_BATCH_SIZE = 1000 # Default batch size when file list is empty + class ImportFile: def __init__(self, upload_key, file_path, local_path): - self.upload_key=upload_key - self.file_path=file_path + self.upload_key = upload_key + self.file_path = file_path self.local_path = local_path + def __repr__(self): return f"ImportFile(upload_key={self.upload_key}, file_path={self.file_path}, local_path={self.local_path})" + class ImportClient(BaseClient): def __init__(self, api_host, session_manager): super().__init__(session_manager) @@ -27,16 +32,13 @@ def __init__(self, api_host, session_manager): def create(self, integration_id, dataset_id, package_id, timeseries_files): url = f"{self.api_host}/import?dataset_id={dataset_id}" - headers = { - "Content-type": "application/json", - "Authorization": f"Bearer {self.session_manager.session_token}" - } + headers = {"Content-type": "application/json", "Authorization": f"Bearer {self.session_manager.session_token}"} body = { "integration_id": integration_id, "package_id": package_id, "import_type": "timeseries", - "files": [{"upload_key": str(file.upload_key), "file_path": file.file_path} for file in timeseries_files] + "files": [{"upload_key": str(file.upload_key), "file_path": file.file_path} for file in timeseries_files], } try: @@ -44,7 +46,7 @@ def create(self, integration_id, dataset_id, package_id, timeseries_files): response.raise_for_status() data = response.json() - return data['id'] + return data["id"] except requests.HTTPError as e: log.error(f"failed to create import with error: {e}") raise e @@ -70,10 +72,7 @@ def append_files(self, import_id, dataset_id, timeseries_files): """ url = f"{self.api_host}/import/{import_id}/files?dataset_id={dataset_id}" - headers = { - "Content-type": "application/json", - "Authorization": f"Bearer {self.session_manager.session_token}" - } + headers = {"Content-type": "application/json", "Authorization": f"Bearer {self.session_manager.session_token}"} body = { "files": [{"upload_key": str(file.upload_key), "file_path": file.file_path} for file in timeseries_files] @@ -117,7 +116,9 @@ def create_batched(self, integration_id, dataset_id, package_id, timeseries_file total_files = len(timeseries_files) total_batches = math.ceil(total_files / batch_size) - log.info(f"dataset_id={dataset_id} creating import manifest with {total_files} files in {total_batches} batch(es) (batch_size={batch_size})") + log.info( + f"dataset_id={dataset_id} creating import manifest with {total_files} files in {total_batches} batch(es) (batch_size={batch_size})" + ) first_batch = timeseries_files[:batch_size] import_id = self.create(integration_id, dataset_id, package_id, first_batch) @@ -138,10 +139,7 @@ def create_batched(self, integration_id, dataset_id, package_id, timeseries_file def get_presign_url(self, import_id, dataset_id, upload_key): url = f"{self.api_host}/import/{import_id}/upload/{upload_key}/presign?dataset_id={dataset_id}" - headers = { - "Content-type": "application/json", - "Authorization": f"Bearer {self.session_manager.session_token}" - } + headers = {"Content-type": "application/json", "Authorization": f"Bearer {self.session_manager.session_token}"} try: response = requests.get(url, headers=headers) @@ -159,6 +157,7 @@ def get_presign_url(self, import_id, dataset_id, upload_key): log.error(f"failed to generate pre-sign URL for import file with error: {e}") raise e + def calculate_batch_size(sample_files, max_size_bytes=MAX_REQUEST_SIZE_BYTES): """ Calculate the optimal batch size for manifest files based on actual payload size. @@ -184,7 +183,7 @@ def calculate_batch_size(sample_files, max_size_bytes=MAX_REQUEST_SIZE_BYTES): # calculate batch size with safety margin (80% of limit) # to allow for request content overhead - usable_size = (max_size_bytes * 0.8) + usable_size = max_size_bytes * 0.8 batch_size = int(usable_size / avg_bytes_per_file) # Ensure at least 1 file per batch diff --git a/processor/clients/timeseries_client.py b/processor/clients/timeseries_client.py index 808ff87..c46cddd 100644 --- a/processor/clients/timeseries_client.py +++ b/processor/clients/timeseries_client.py @@ -1,12 +1,15 @@ -import requests import json import logging -from .base_client import BaseClient +import requests + from processor.timeseries_channel import TimeSeriesChannel +from .base_client import BaseClient + log = logging.getLogger() + class TimeSeriesClient(BaseClient): def __init__(self, api_host, session_manager): super().__init__(session_manager) @@ -17,19 +20,16 @@ def __init__(self, api_host, session_manager): def create_channel(self, package_id, channel): url = f"{self.api_host}/timeseries/{package_id}/channels" - headers = { - "Content-type": "application/json", - "Authorization": f"Bearer {self.session_manager.session_token}" - } + headers = {"Content-type": "application/json", "Authorization": f"Bearer {self.session_manager.session_token}"} body = channel.as_dict() - body['channelType'] = body.pop('type') + body["channelType"] = body.pop("type") try: response = requests.post(url, headers=headers, json=body) response.raise_for_status() data = response.json() - created_channel = TimeSeriesChannel.from_dict(data['content'], data['properties']) + created_channel = TimeSeriesChannel.from_dict(data["content"], data["properties"]) created_channel.index = channel.index return created_channel @@ -47,10 +47,7 @@ def create_channel(self, package_id, channel): def get_package_channels(self, package_id): url = f"{self.api_host}/timeseries/{package_id}/channels" - headers = { - "Content-type": "application/json", - "Authorization": f"Bearer {self.session_manager.session_token}" - } + headers = {"Content-type": "application/json", "Authorization": f"Bearer {self.session_manager.session_token}"} try: response = requests.get(url, headers=headers) diff --git a/processor/clients/workflow_client.py b/processor/clients/workflow_client.py index 8f6664a..12d3d19 100644 --- a/processor/clients/workflow_client.py +++ b/processor/clients/workflow_client.py @@ -1,17 +1,20 @@ -import requests import json import logging +import requests + from .base_client import BaseClient log = logging.getLogger() + class WorkflowInstance: def __init__(self, id, dataset_id, package_ids): self.id = id self.dataset_id = dataset_id self.package_ids = package_ids + class WorkflowClient(BaseClient): def __init__(self, api_host, session_manager): super().__init__(session_manager) @@ -24,10 +27,7 @@ def __init__(self, api_host, session_manager): def get_workflow_instance(self, workflow_instance_id): url = f"{self.api_host}/workflows/instances/{workflow_instance_id}" - headers = { - "Accept": "application/json", - "Authorization": f"Bearer {self.session_manager.session_token}" - } + headers = {"Accept": "application/json", "Authorization": f"Bearer {self.session_manager.session_token}"} try: response = requests.get(url, headers=headers) diff --git a/processor/config.py b/processor/config.py index 565c82a..95b8a5b 100644 --- a/processor/config.py +++ b/processor/config.py @@ -1,34 +1,36 @@ import os import uuid + class Config: def __init__(self): - self.ENVIRONMENT = os.getenv('ENVIRONMENT', 'local') + self.ENVIRONMENT = os.getenv("ENVIRONMENT", "local") - if self.ENVIRONMENT == 'local': - self.INPUT_DIR = os.getenv('INPUT_DIR') - self.OUTPUT_DIR = os.getenv('OUTPUT_DIR') + if self.ENVIRONMENT == "local": + self.INPUT_DIR = os.getenv("INPUT_DIR") + self.OUTPUT_DIR = os.getenv("OUTPUT_DIR") else: # workflow / analysis pipeline only supports 3 processors (pre-, main, post-) # the output directory of the main processor is what the post-processor needs to read from # so for now we will set the input directory for this processor to be the output directory variable - self.INPUT_DIR = os.getenv('OUTPUT_DIR') - self.OUTPUT_DIR = os.path.join(self.INPUT_DIR, "output") + self.INPUT_DIR = os.getenv("OUTPUT_DIR") + self.OUTPUT_DIR = os.path.join(self.INPUT_DIR, "output") if not os.path.exists(self.OUTPUT_DIR): os.makedirs(self.OUTPUT_DIR) - self.CHUNK_SIZE_MB = int(os.getenv('CHUNK_SIZE_MB', '1')) + self.CHUNK_SIZE_MB = int(os.getenv("CHUNK_SIZE_MB", "1")) # continue to use INTEGRATION_ID environment variable until runner # has been converted to use a different variable to represent the workflow instance ID - self.WORKFLOW_INSTANCE_ID = os.getenv('INTEGRATION_ID', str(uuid.uuid4())) + self.WORKFLOW_INSTANCE_ID = os.getenv("INTEGRATION_ID", str(uuid.uuid4())) + + self.API_KEY = os.getenv("PENNSIEVE_API_KEY") + self.API_SECRET = os.getenv("PENNSIEVE_API_SECRET") + self.API_HOST = os.getenv("PENNSIEVE_API_HOST", "https://api.pennsieve.net") + self.API_HOST2 = os.getenv("PENNSIEVE_API_HOST2", "https://api2.pennsieve.net") - self.API_KEY = os.getenv('PENNSIEVE_API_KEY') - self.API_SECRET = os.getenv('PENNSIEVE_API_SECRET') - self.API_HOST = os.getenv('PENNSIEVE_API_HOST', 'https://api.pennsieve.net') - self.API_HOST2 = os.getenv('PENNSIEVE_API_HOST2', 'https://api2.pennsieve.net') + self.IMPORTER_ENABLED = getboolenv("IMPORTER_ENABLED", self.ENVIRONMENT != "local") - self.IMPORTER_ENABLED = getboolenv("IMPORTER_ENABLED", self.ENVIRONMENT != 'local') def getboolenv(key, default=False): - return os.getenv(key, str(default)).lower() in ('true', '1') + return os.getenv(key, str(default)).lower() in ("true", "1") diff --git a/processor/constants.py b/processor/constants.py index 959c671..c200b3e 100644 --- a/processor/constants.py +++ b/processor/constants.py @@ -1,2 +1,2 @@ -TIME_SERIES_BINARY_FILE_EXTENSION='.bin.gz' -TIME_SERIES_METADATA_FILE_EXTENSION='.metadata.json' +TIME_SERIES_BINARY_FILE_EXTENSION = ".bin.gz" +TIME_SERIES_METADATA_FILE_EXTENSION = ".metadata.json" diff --git a/processor/importer.py b/processor/importer.py index d933cf2..739bffd 100644 --- a/processor/importer.py +++ b/processor/importer.py @@ -1,25 +1,18 @@ -import backoff +import json import logging import os -import json import re -import requests import uuid +from concurrent.futures import ThreadPoolExecutor +from multiprocessing import Lock, Value -from clients import AuthenticationClient, SessionManager -from clients import ImportClient, ImportFile -from clients import SessionManager -from clients import TimeSeriesClient -from clients import WorkflowClient, WorkflowInstance - +import backoff +import requests +from clients import AuthenticationClient, ImportClient, ImportFile, SessionManager, TimeSeriesClient, WorkflowClient from constants import TIME_SERIES_BINARY_FILE_EXTENSION, TIME_SERIES_METADATA_FILE_EXTENSION - from timeseries_channel import TimeSeriesChannel -from concurrent.futures import ThreadPoolExecutor -from multiprocessing import Value, Lock - -logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s') +logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s") log = logging.getLogger() @@ -31,6 +24,7 @@ # easily able to handle > 3 processors """ + def import_timeseries(api_host, api2_host, api_key, api_secret, workflow_instance_id, file_directory): # gather all the time series files from the output directory timeseries_data_files = [] @@ -53,7 +47,7 @@ def import_timeseries(api_host, api2_host, api_key, api_secret, workflow_instanc # fetch workflow instance for parameters (dataset_id, package_id, etc.) workflow_client = WorkflowClient(api2_host, session_manager) - workflow_instance = workflow_client.get_workflow_instance(workflow_instance_id) + workflow_instance = workflow_client.get_workflow_instance(workflow_instance_id) # constraint until we implement (upstream) performing imports over directories # and specifying how to group time series files together into an imported package @@ -72,10 +66,12 @@ def import_timeseries(api_host, api2_host, api_key, api_secret, workflow_instanc for file_path in timeseries_channel_files: channel_index = channel_index_pattern.search(os.path.basename(file_path)).group(1) - with open(file_path, 'r') as file: + with open(file_path, "r") as file: local_channel = TimeSeriesChannel.from_dict(json.load(file)) - channel = next((existing_channel for existing_channel in existing_channels if existing_channel == local_channel), None) + channel = next( + (existing_channel for existing_channel in existing_channels if existing_channel == local_channel), None + ) if channel is not None: log.info(f"package_id={package_id} channel_id={channel.id} found existing package channel: {channel.name}") else: @@ -95,43 +91,48 @@ def import_timeseries(api_host, api2_host, api_key, api_secret, workflow_instanc import_file = ImportFile( upload_key=uuid.uuid4(), file_path=re.sub(channel_index_pattern, channel.id, os.path.basename(file_path)), - local_path = file_path + local_path=file_path, ) import_files.append(import_file) # initialize import with batched manifest creation to avoid API Gateway size limits import_client = ImportClient(api2_host, session_manager) - import_id = import_client.create_batched(workflow_instance.id, workflow_instance.dataset_id, package_id, import_files) + import_id = import_client.create_batched( + workflow_instance.id, workflow_instance.dataset_id, package_id, import_files + ) log.info(f"import_id={import_id} initialized import with {len(import_files)} time series data files for upload") # track time series file upload count - upload_counter = Value('i', 0) + upload_counter = Value("i", 0) upload_counter_lock = Lock() # upload time series files to Pennsieve S3 import bucket - @backoff.on_exception( - backoff.expo, - requests.exceptions.RequestException, - max_tries=5 - ) + @backoff.on_exception(backoff.expo, requests.exceptions.RequestException, max_tries=5) def upload_timeseries_file(timeseries_file): try: with upload_counter_lock: upload_counter.value += 1 - log.info(f"import_id={import_id} upload_key={timeseries_file.upload_key} uploading {upload_counter.value}/{len(import_files)} {timeseries_file.local_path}") - upload_url = import_client.get_presign_url(import_id, workflow_instance.dataset_id, timeseries_file.upload_key) - with open(timeseries_file.local_path, 'rb') as f: + log.info( + f"import_id={import_id} upload_key={timeseries_file.upload_key} uploading {upload_counter.value}/{len(import_files)} {timeseries_file.local_path}" + ) + upload_url = import_client.get_presign_url( + import_id, workflow_instance.dataset_id, timeseries_file.upload_key + ) + with open(timeseries_file.local_path, "rb") as f: response = requests.put(upload_url, data=f) response.raise_for_status() # raise an error if the request failed return True except Exception as e: with upload_counter_lock: upload_counter.value -= 1 - log.error(f"import_id={import_id} upload_key={timeseries_file.upload_key} failed to upload {timeseries_file.local_path}: %s", e) + log.error( + f"import_id={import_id} upload_key={timeseries_file.upload_key} failed to upload {timeseries_file.local_path}: %s", + e, + ) raise e - successful_uploads = list() + successful_uploads = [] with ThreadPoolExecutor(max_workers=4) as executor: # wrapping in a list forces the executor to wait for all threads to finish uploading time series files successful_uploads = list(executor.map(upload_timeseries_file, import_files)) diff --git a/processor/main.py b/processor/main.py index e36c56f..3677fcd 100644 --- a/processor/main.py +++ b/processor/main.py @@ -1,15 +1,14 @@ -import os import logging +import os import time -from pynwb import NWBHDF5IO -from pynwb.ecephys import ElectricalSeries - from config import Config from importer import import_timeseries +from pynwb import NWBHDF5IO +from pynwb.ecephys import ElectricalSeries from writer import TimeSeriesChunkWriter -logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s') +logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s") log = logging.getLogger() @@ -17,24 +16,22 @@ config = Config() bytes_per_mb = pow(2, 20) - bytes_per_sample = 8 # 64-bit floating point value + bytes_per_sample = 8 # 64-bit floating point value chunk_size = int(config.CHUNK_SIZE_MB * bytes_per_mb / bytes_per_sample) input_files = [ - f.path - for f in os.scandir(config.INPUT_DIR) - if f.is_file() and os.path.splitext(f.name)[1].lower() == '.nwb' + f.path for f in os.scandir(config.INPUT_DIR) if f.is_file() and os.path.splitext(f.name)[1].lower() == ".nwb" ] assert len(input_files) == 1, "NWB post processor only supports a single file as input" with NWBHDF5IO(input_files[0], mode="r") as io: nwb = io.read() - electrical_series = [acq for acq in nwb.acquisition.values() if type(acq) == ElectricalSeries] + electrical_series = [acq for acq in nwb.acquisition.values() if isinstance(acq, ElectricalSeries)] if len(electrical_series) < 1: - log.error('NWB file has no continuous raw electrical series data') + log.error("NWB file has no continuous raw electrical series data") if len(electrical_series) > 1: - log.warn('NWB file has multiple raw electrical series acquisitions') + log.warn("NWB file has multiple raw electrical series acquisitions") chunked_writer = TimeSeriesChunkWriter(nwb.session_start_time, config.OUTPUT_DIR, chunk_size) @@ -48,4 +45,11 @@ # note: this will be moved to a separated post-processor once the analysis pipeline is more # easily able to handle > 3 processors if config.IMPORTER_ENABLED: - importer = import_timeseries(config.API_HOST, config.API_HOST2, config.API_KEY, config.API_SECRET, config.WORKFLOW_INSTANCE_ID, config.OUTPUT_DIR) + importer = import_timeseries( + config.API_HOST, + config.API_HOST2, + config.API_KEY, + config.API_SECRET, + config.WORKFLOW_INSTANCE_ID, + config.OUTPUT_DIR, + ) diff --git a/processor/reader.py b/processor/reader.py index 15196c2..ec45fce 100644 --- a/processor/reader.py +++ b/processor/reader.py @@ -1,13 +1,13 @@ import logging -import numpy as np +import numpy as np from pandas import DataFrame, Series -from pynwb.ecephys import ElectricalSeries from timeseries_channel import TimeSeriesChannel from utils import infer_sampling_rate log = logging.getLogger() + class NWBElectricalSeriesReader: """ Wrapper class around the NWB ElectricalSeries object. @@ -28,8 +28,10 @@ def __init__(self, electrical_series, session_start_time): self.session_start_time_secs = session_start_time.timestamp() self.num_samples, self.num_channels = self.electrical_series.data.shape - assert self.num_samples > 0, 'Electrical series has no sample data' - assert len(self.electrical_series.electrodes.table) == self.num_channels, 'Electrode channels do not align with data shape' + assert self.num_samples > 0, "Electrical series has no sample data" + assert ( + len(self.electrical_series.electrodes.table) == self.num_channels + ), "Electrode channels do not align with data shape" self._sampling_rate = None self._timestamps = None @@ -39,7 +41,6 @@ def __init__(self, electrical_series, session_start_time): self._channels = None - def _compute_sampling_rate_and_timestamps(self): """ Sets the sampling_rate and timestamps properties on the reader object. @@ -65,17 +66,20 @@ def _compute_sampling_rate_and_timestamps(self): sampling_rate = self.electrical_series.rate inferred_sampling_rate = infer_sampling_rate(timestamps) - error = abs(inferred_sampling_rate-sampling_rate) * (1.0 / sampling_rate) + error = abs(inferred_sampling_rate - sampling_rate) * (1.0 / sampling_rate) if error > 0.02: # error is greater than 2% - raise Exception("Inferred rate from timestamps ({inferred_rate:.4f}) does not match given rate ({given_rate:.4f})." \ - .format(inferred_rate=inferred_sampling_rate, given_rate=sampling_rate)) + raise Exception( + "Inferred rate from timestamps ({inferred_rate:.4f}) does not match given rate ({given_rate:.4f}).".format( + inferred_rate=inferred_sampling_rate, given_rate=sampling_rate + ) + ) # if only the rate is given, calculate the timestamps for the samples # using the given number of samples (size of the data) if self.electrical_series.rate: sampling_rate = self.electrical_series.rate - timestamps = np.linspace(0, self.num_samples / sampling_rate, self.num_samples, endpoint = False) + timestamps = np.linspace(0, self.num_samples / sampling_rate, self.num_samples, endpoint=False) # if only the timestamps are given, calculate the sampling rate using the timestamps if self.electrical_series.timestamps: @@ -96,14 +100,14 @@ def sampling_rate(self): @property def channels(self): if not self._channels: - channels = list() + channels = [] for index, electrode in enumerate(self.electrical_series.electrodes): name = "" if isinstance(electrode, DataFrame): - if 'channel_name' in electrode: - name = electrode['channel_name'] - elif 'label' in electrode: - name = electrode['label'] + if "channel_name" in electrode: + name = electrode["channel_name"] + elif "label" in electrode: + name = electrode["label"] if isinstance(name, Series): name = name.iloc[0] @@ -113,16 +117,16 @@ def channels(self): group_name = group_name.iloc[0] channels.append( - # convert start / end to microseconds to maintain precision - TimeSeriesChannel( - index = index, - name = name, - rate = self.sampling_rate, - start = self.timestamps[0] * 1e6 , # safe access gaurenteed by initialization assertions - end = self.timestamps[-1] * 1e6, - group = group_name - ) + # convert start / end to microseconds to maintain precision + TimeSeriesChannel( + index=index, + name=name, + rate=self.sampling_rate, + start=self.timestamps[0] * 1e6, # safe access gaurenteed by initialization assertions + end=self.timestamps[-1] * 1e6, + group=group_name, ) + ) self._channels = channels @@ -143,12 +147,13 @@ def contiguous_chunks(self): gap_threshold = (1.0 / self.sampling_rate) * 2 boundaries = np.concatenate( - ([0], (np.diff(self.timestamps) > gap_threshold).nonzero()[0] + 1, [len(self.timestamps)])) + ([0], (np.diff(self.timestamps) > gap_threshold).nonzero()[0] + 1, [len(self.timestamps)]) + ) - for i in np.arange(len(boundaries)-1): + for i in np.arange(len(boundaries) - 1): yield boundaries[i], boundaries[i + 1] - def get_chunk(self, channel_index, start = None, end = None): + def get_chunk(self, channel_index, start=None, end=None): """ Returns a chunk of sample data from the electrical series for the given channel (index) diff --git a/processor/timeseries_channel.py b/processor/timeseries_channel.py index 4109a86..62408fd 100644 --- a/processor/timeseries_channel.py +++ b/processor/timeseries_channel.py @@ -1,65 +1,79 @@ -import os -import uuid - class TimeSeriesChannel: - def __init__(self, index, name, rate, start, end, type = 'CONTINUOUS', unit = 'uV', group='default', last_annotation=0, properties=[], id=None): - assert type.upper() in ['CONTINUOUS', 'UNIT'], "Type must be CONTINUOUS or UNIT" + def __init__( + self, + index, + name, + rate, + start, + end, + type="CONTINUOUS", + unit="uV", + group="default", + last_annotation=0, + properties=None, + id=None, + ): + if properties is None: + properties = [] + assert type.upper() in ["CONTINUOUS", "UNIT"], "Type must be CONTINUOUS or UNIT" # metadata for intra-processor tracking - self.index = index + self.index = index - self.id = id - self.name = name.strip() - self.rate = rate + self.id = id + self.name = name.strip() + self.rate = rate - self.start = int(start) - self.end = int(end) + self.start = int(start) + self.end = int(end) - self.unit = unit.strip() - self.type = type.upper() - self.group = group.strip() + self.unit = unit.strip() + self.type = type.upper() + self.group = group.strip() self.last_annotation = last_annotation self.properties = properties def as_dict(self): resp = { - 'name': self.name, - 'start': self.start, - 'end': self.end, - 'unit': self.unit, - 'rate': self.rate, - 'type': self.type, - 'group': self.group, - 'lastAnnotation': self.last_annotation, - 'properties': self.properties + "name": self.name, + "start": self.start, + "end": self.end, + "unit": self.unit, + "rate": self.rate, + "type": self.type, + "group": self.group, + "lastAnnotation": self.last_annotation, + "properties": self.properties, } if self.id is not None: - resp['id'] = self.id + resp["id"] = self.id return resp @staticmethod def from_dict(channel, properties=None): return TimeSeriesChannel( - name = channel['name'], - start = int(channel['start']), - end = int(channel['end']), - unit = channel['unit'], - rate = channel['rate'], - type = channel.get('channelType', channel.get('type')), - group = channel['group'], - last_annotation = int(channel.get('lastAnnotation', 0)), - properties = channel.get('properties', properties), - id = channel.get('id'), - index = -1, + name=channel["name"], + start=int(channel["start"]), + end=int(channel["end"]), + unit=channel["unit"], + rate=channel["rate"], + type=channel.get("channelType", channel.get("type")), + group=channel["group"], + last_annotation=int(channel.get("lastAnnotation", 0)), + properties=channel.get("properties", properties), + id=channel.get("id"), + index=-1, ) # custom equality on time series channels for comparing new vs. existing channels # equal when name and type are equal and rate is within a small bounded range def __eq__(self, other): - return all([ - self.name.casefold() == other.name.casefold(), - self.type.casefold() == other.type.casefold(), - abs(1-(self.rate/other.rate)) < 0.02 - ]) + return all( + [ + self.name.casefold() == other.name.casefold(), + self.type.casefold() == other.type.casefold(), + abs(1 - (self.rate / other.rate)) < 0.02, + ] + ) diff --git a/processor/utils.py b/processor/utils.py index 5765cc2..1019040 100644 --- a/processor/utils.py +++ b/processor/utils.py @@ -2,6 +2,7 @@ import numpy as np + def infer_sampling_rate(timestamps): """ Derives a sampling rate based on timestamps given in seconds. @@ -11,8 +12,9 @@ def infer_sampling_rate(timestamps): sampling_period = np.median(np.diff(timestamps[:10])) return 1 / sampling_period + def to_big_endian(data): - if data.dtype.byteorder == '<' or (data.dtype.byteorder == '=' and sys.byteorder == 'little'): + if data.dtype.byteorder == "<" or (data.dtype.byteorder == "=" and sys.byteorder == "little"): return data.byteswap(True).view(data.dtype.newbyteorder()) else: return data diff --git a/processor/writer.py b/processor/writer.py index a6c578c..66cf410 100644 --- a/processor/writer.py +++ b/processor/writer.py @@ -1,15 +1,16 @@ import gzip import json import logging -import numpy as np import os +import numpy as np from constants import TIME_SERIES_BINARY_FILE_EXTENSION, TIME_SERIES_METADATA_FILE_EXTENSION from reader import NWBElectricalSeriesReader from utils import to_big_endian log = logging.getLogger() + class TimeSeriesChunkWriter: """ Attributes: @@ -38,7 +39,7 @@ def write_electrical_series(self, electrical_series): chunk_end = min(contiguous_end, chunk_start + self.chunk_size) start_time = reader.timestamps[chunk_start] - end_time = reader.timestamps[chunk_end-1] + end_time = reader.timestamps[chunk_end - 1] for channel_index in range(len(reader.channels)): chunk = reader.get_chunk(channel_index, chunk_start, chunk_end) @@ -55,18 +56,20 @@ def write_chunk(self, chunk, start_time, end_time, channel): Writes the chunked sample data to a gzipped binary file. """ # ensure the samples are 64-bit float-pointing numbers in big-endian before converting to bytes - formatted_data = to_big_endian(chunk.astype(np.float64)) + formatted_data = to_big_endian(chunk.astype(np.float64)) - channel_index = '{index:05d}'.format(index=channel.index) - file_name = "channel-{}_{}_{}{}".format(channel_index, int(start_time * 1e6), int(end_time * 1e6), TIME_SERIES_BINARY_FILE_EXTENSION) + channel_index = "{index:05d}".format(index=channel.index) + file_name = "channel-{}_{}_{}{}".format( + channel_index, int(start_time * 1e6), int(end_time * 1e6), TIME_SERIES_BINARY_FILE_EXTENSION + ) file_path = os.path.join(self.output_dir, file_name) - with gzip.open(file_path, mode='wb', compresslevel=1) as f: + with gzip.open(file_path, mode="wb", compresslevel=1) as f: f.write(formatted_data) def write_channel(self, channel): - file_name = f'channel-{channel.index:05d}{TIME_SERIES_METADATA_FILE_EXTENSION}' + file_name = f"channel-{channel.index:05d}{TIME_SERIES_METADATA_FILE_EXTENSION}" file_path = os.path.join(self.output_dir, file_name) - with open(file_path, 'w') as file: + with open(file_path, "w") as file: json.dump(channel.as_dict(), file) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..449a551 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,70 @@ +[project] +name = "processor-post-timeseries" +version = "1.0.0" +description = "NWB file post-processor for extracting and uploading timeseries data to Pennsieve" +requires-python = ">=3.10" +dependencies = [ + "numpy", + "pynwb", + "requests", + "boto3", + "backoff", +] + +[project.optional-dependencies] +test = [ + "pytest>=7.0.0", + "pytest-cov>=4.0.0", + "pytest-mock>=3.10.0", + "responses>=0.23.0", +] +dev = [ + "ruff", +] + +[tool.pytest.ini_options] +testpaths = ["tests"] +python_files = ["test_*.py"] +python_classes = ["Test*"] +python_functions = ["test_*"] +addopts = "-v --tb=short" +filterwarnings = [ + "ignore::DeprecationWarning", +] + +[tool.coverage.run] +source = ["processor"] +omit = [ + "processor/__init__.py", + "processor/main.py", +] + +[tool.coverage.report] +exclude_lines = [ + "pragma: no cover", + "def __repr__", + "raise AssertionError", + "raise NotImplementedError", + "if __name__ == .__main__.:", +] + +[tool.ruff] +target-version = "py310" +line-length = 120 + +[tool.ruff.lint] +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # pyflakes + "I", # isort + "B", # flake8-bugbear + "C4", # flake8-comprehensions +] +ignore = [ + "E501", # line too long (handled by formatter) + "B008", # do not perform function calls in argument defaults +] + +[tool.ruff.lint.per-file-ignores] +"tests/*" = ["B", "C4"] diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 0000000..ee23f6c --- /dev/null +++ b/pytest.ini @@ -0,0 +1,8 @@ +[pytest] +testpaths = tests +python_files = test_*.py +python_classes = Test* +python_functions = test_* +addopts = -v --tb=short +filterwarnings = + ignore::DeprecationWarning diff --git a/requirements-test.txt b/requirements-test.txt new file mode 100644 index 0000000..9937f0e --- /dev/null +++ b/requirements-test.txt @@ -0,0 +1,6 @@ +pytest>=7.0.0 +pytest-cov>=4.0.0 +pytest-mock>=3.10.0 +responses>=0.23.0 +pre-commit>=3.5.0 +ruff>=0.8.0 diff --git a/scripts/generate_test_nwb.py b/scripts/generate_test_nwb.py new file mode 100644 index 0000000..502a0ba --- /dev/null +++ b/scripts/generate_test_nwb.py @@ -0,0 +1,286 @@ +#!/usr/bin/env python3 +""" +Generate a test NWB file with two channels of sine wave timeseries data. + +This script creates an NWB file compatible with the processor-post-timeseries +processor. The file contains two channels with sine waves at different frequencies. + +Usage: + python3 generate_test_nwb.py --size 10MB --output test.nwb + python3 generate_test_nwb.py --size 1GB --output large_test.nwb + python3 generate_test_nwb.py --size 50GB --output huge_test.nwb + +Size format: where unit is B, KB, MB, GB, or TB +""" + +import argparse +import re +import sys +from datetime import datetime, timezone +from pathlib import Path + +import numpy as np +from pynwb import NWBHDF5IO, NWBFile +from pynwb.ecephys import ElectricalSeries + + +def parse_size(size_str: str) -> int: + """Parse a human-readable size string into bytes.""" + units = { + "B": 1, + "KB": 1024, + "MB": 1024**2, + "GB": 1024**3, + "TB": 1024**4, + } + + match = re.match(r"^(\d+(?:\.\d+)?)\s*(B|KB|MB|GB|TB)$", size_str.upper().strip()) + if not match: + raise ValueError(f"Invalid size format: '{size_str}'. Use format like '10MB', '1GB', '50GB'") + + value = float(match.group(1)) + unit = match.group(2) + + return int(value * units[unit]) + + +def calculate_samples_for_size(target_bytes: int, num_channels: int = 2) -> int: + """ + Calculate the number of samples needed to achieve target file size. + + NWB stores data as 64-bit floats (8 bytes per value). + With HDF5 overhead, actual file size is slightly larger than raw data. + We account for ~5% overhead for HDF5 metadata and structure. + """ + bytes_per_sample = 8 * num_channels # 8 bytes per float64, per channel + overhead_factor = 0.95 # Account for HDF5 overhead + + effective_data_bytes = target_bytes * overhead_factor + num_samples = int(effective_data_bytes / bytes_per_sample) + + return max(num_samples, 1000) # Minimum 1000 samples + + +def generate_sine_wave( + num_samples: int, frequency: float, sampling_rate: float, amplitude: float = 100.0, phase: float = 0.0 +) -> np.ndarray: + """ + Generate a sine wave signal. + + Args: + num_samples: Number of samples to generate + frequency: Frequency of the sine wave in Hz + sampling_rate: Sampling rate in Hz + amplitude: Peak amplitude of the sine wave (in microvolts) + phase: Phase offset in radians + + Returns: + numpy array of float64 values + """ + t = np.arange(num_samples) / sampling_rate + return amplitude * np.sin(2 * np.pi * frequency * t + phase) + + +def create_nwb_file( + output_path: str, target_size_bytes: int, freq1: float = 10.0, freq2: float = 25.0, sampling_rate: float = 1000.0 +) -> dict: + """ + Create an NWB file with two channels of sine wave data. + + Args: + output_path: Path to save the NWB file + target_size_bytes: Target file size in bytes + freq1: Frequency of channel 1 sine wave (Hz) + freq2: Frequency of channel 2 sine wave (Hz) + sampling_rate: Sampling rate for both channels (Hz) + + Returns: + Dictionary with metadata about the created file + """ + num_channels = 2 + num_samples = calculate_samples_for_size(target_size_bytes, num_channels) + duration_seconds = num_samples / sampling_rate + + print("Generating NWB file with:") + print(f" Target size: {target_size_bytes / (1024**2):.2f} MB") + print(f" Samples: {num_samples:,}") + print(f" Duration: {duration_seconds:.2f} seconds ({duration_seconds/3600:.2f} hours)") + print(f" Sampling rate: {sampling_rate} Hz") + print(f" Channel 1 frequency: {freq1} Hz") + print(f" Channel 2 frequency: {freq2} Hz") + print() + + # Generate sine wave data for both channels + print("Generating sine wave data...") + channel1_data = generate_sine_wave(num_samples, freq1, sampling_rate, amplitude=100.0) + channel2_data = generate_sine_wave(num_samples, freq2, sampling_rate, amplitude=150.0, phase=np.pi / 4) + + # Stack into shape (num_samples, num_channels) + data = np.column_stack([channel1_data, channel2_data]) + print(f" Data shape: {data.shape}") + print(f" Data size: {data.nbytes / (1024**2):.2f} MB") + + # Create NWB file + print("\nCreating NWB file structure...") + session_start_time = datetime(2024, 1, 1, 0, 0, 0, tzinfo=timezone.utc) + + nwbfile = NWBFile( + session_description="Test NWB file with sine wave timeseries data", + identifier=f"test_nwb_{datetime.now().strftime('%Y%m%d_%H%M%S')}", + session_start_time=session_start_time, + experimenter=["Test Generator"], + lab="Test Lab", + institution="Test Institution", + experiment_description="Generated test data with two sine wave channels", + ) + + # Create device + device = nwbfile.create_device( + name="TestDevice", + description="Virtual test device for generating sine wave data", + manufacturer="Test Manufacturer", + ) + + # Create electrode group + electrode_group = nwbfile.create_electrode_group( + name="TestElectrodeGroup", + description="Test electrode group with two channels", + location="Test Location", + device=device, + ) + + # Add electrodes to the electrode table + # The processor expects 'channel_name' or 'label' column and 'group_name' + nwbfile.add_electrode_column(name="channel_name", description="Name of the electrode channel") + + nwbfile.add_electrode( + x=0.0, + y=0.0, + z=0.0, + imp=1000.0, + location="Test Location 1", + filtering="None", + group=electrode_group, + channel_name=f"SineWave_{freq1}Hz", + ) + + nwbfile.add_electrode( + x=1.0, + y=0.0, + z=0.0, + imp=1000.0, + location="Test Location 2", + filtering="None", + group=electrode_group, + channel_name=f"SineWave_{freq2}Hz", + ) + + # Create electrode table region for all electrodes + electrode_table_region = nwbfile.create_electrode_table_region(region=[0, 1], description="All test electrodes") + + # Create ElectricalSeries with the sine wave data + electrical_series = ElectricalSeries( + name="TestElectricalSeries", + description="Two channels of sine wave data at different frequencies", + data=data, + electrodes=electrode_table_region, + rate=sampling_rate, + conversion=1e-6, # Data is in microvolts, conversion to volts + offset=0.0, + starting_time=0.0, + ) + + # Add to acquisition + nwbfile.add_acquisition(electrical_series) + + # Write the file + print(f"Writing NWB file to: {output_path}") + output_path = Path(output_path) + output_path.parent.mkdir(parents=True, exist_ok=True) + + with NWBHDF5IO(str(output_path), mode="w") as io: + io.write(nwbfile) + + actual_size = output_path.stat().st_size + print("\nFile created successfully!") + print(f" Actual file size: {actual_size / (1024**2):.2f} MB") + print(f" Size ratio: {actual_size / target_size_bytes:.2%} of target") + + return { + "output_path": str(output_path), + "target_size_bytes": target_size_bytes, + "actual_size_bytes": actual_size, + "num_samples": num_samples, + "num_channels": num_channels, + "duration_seconds": duration_seconds, + "sampling_rate": sampling_rate, + "channel_frequencies": [freq1, freq2], + } + + +def main(): + parser = argparse.ArgumentParser( + description="Generate a test NWB file with sine wave timeseries data", + formatter_class=argparse.RawDescriptionHelpFormatter, + epilog=""" +Examples: + %(prog)s --size 10MB --output test.nwb + %(prog)s --size 1GB --output large_test.nwb + %(prog)s --size 50GB --output huge_test.nwb + %(prog)s --size 100MB --freq1 5 --freq2 50 --rate 2000 --output custom.nwb + """, + ) + + parser.add_argument("--size", "-s", required=True, help="Target file size (e.g., '10MB', '1GB', '50GB')") + + parser.add_argument("--output", "-o", required=True, help="Output NWB file path") + + parser.add_argument( + "--freq1", type=float, default=10.0, help="Frequency of channel 1 sine wave in Hz (default: 10.0)" + ) + + parser.add_argument( + "--freq2", type=float, default=25.0, help="Frequency of channel 2 sine wave in Hz (default: 25.0)" + ) + + parser.add_argument("--rate", type=float, default=1000.0, help="Sampling rate in Hz (default: 1000.0)") + + args = parser.parse_args() + + try: + target_size = parse_size(args.size) + except ValueError as e: + print(f"Error: {e}", file=sys.stderr) + sys.exit(1) + + # Validate frequencies against Nyquist + nyquist = args.rate / 2 + if args.freq1 >= nyquist or args.freq2 >= nyquist: + print(f"Error: Frequencies must be less than Nyquist frequency ({nyquist} Hz)", file=sys.stderr) + print(" Increase --rate or decrease --freq1/--freq2", file=sys.stderr) + sys.exit(1) + + try: + result = create_nwb_file( + output_path=args.output, + target_size_bytes=target_size, + freq1=args.freq1, + freq2=args.freq2, + sampling_rate=args.rate, + ) + + print("\nFile metadata summary:") + print(f" Path: {result['output_path']}") + print(f" Channels: {result['num_channels']}") + print(f" Samples per channel: {result['num_samples']:,}") + print(f" Duration: {result['duration_seconds']:.2f}s ({result['duration_seconds']/3600:.2f}h)") + print(f" Sampling rate: {result['sampling_rate']} Hz") + print(f" Channel frequencies: {result['channel_frequencies']} Hz") + + except Exception as e: + print(f"Error creating NWB file: {e}", file=sys.stderr) + sys.exit(1) + + +if __name__ == "__main__": + main() diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..66173ae --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1 @@ +# Test package diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..5a1410b --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,141 @@ +import os +import sys +from datetime import datetime +from unittest.mock import Mock + +import numpy as np +import pytest + +# Add processor directory to path for imports +sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", "processor")) + + +@pytest.fixture +def sample_channel_dict(): + """Sample channel dictionary as returned from API.""" + return { + "name": "Channel 1", + "start": 1000000, + "end": 2000000, + "unit": "uV", + "rate": 30000.0, + "type": "CONTINUOUS", + "group": "default", + "lastAnnotation": 0, + "properties": [], + "id": "N:channel:test-id-123", + } + + +@pytest.fixture +def sample_channel_dict_with_channel_type(): + """Sample channel dictionary with channelType key (API response format).""" + return { + "name": "Channel 1", + "start": 1000000, + "end": 2000000, + "unit": "uV", + "rate": 30000.0, + "channelType": "CONTINUOUS", + "group": "default", + "lastAnnotation": 0, + "properties": [], + "id": "N:channel:test-id-123", + } + + +@pytest.fixture +def mock_session_manager(): + """Mock session manager for API clients.""" + manager = Mock() + manager.session_token = "mock-token-12345" + manager.refresh_session = Mock() + return manager + + +@pytest.fixture +def mock_authentication_client(): + """Mock authentication client.""" + client = Mock() + client.authenticate = Mock(return_value="mock-access-token") + return client + + +@pytest.fixture +def sample_timestamps(): + """Sample evenly-spaced timestamps at 1000 Hz.""" + return np.linspace(0, 1.0, 1000, endpoint=False) + + +@pytest.fixture +def sample_timestamps_with_gap(): + """Sample timestamps with a gap in the middle (for contiguous chunk testing).""" + # First 500 samples at 1000 Hz (0 to 0.5 seconds) + first_segment = np.linspace(0, 0.5, 500, endpoint=False) + # Gap of 0.1 seconds, then another 500 samples + second_segment = np.linspace(0.6, 1.1, 500, endpoint=False) + return np.concatenate([first_segment, second_segment]) + + +@pytest.fixture +def sample_electrical_series_data(): + """Sample 2D array of electrical series data (samples x channels).""" + np.random.seed(42) + return np.random.randn(1000, 4).astype(np.float64) + + +@pytest.fixture +def mock_electrical_series(sample_electrical_series_data, sample_timestamps): + """Mock pynwb ElectricalSeries object.""" + series = Mock() + series.data = sample_electrical_series_data + series.rate = 1000.0 + series.timestamps = None + series.conversion = 1.0 + series.offset = 0.0 + series.channel_conversion = None + + # Mock electrodes table + mock_electrodes = [] + for i in range(4): + electrode = Mock() + electrode.group_name = f"group_{i}" + mock_electrodes.append(electrode) + + series.electrodes = mock_electrodes + series.electrodes.table = mock_electrodes + + return series + + +@pytest.fixture +def temp_output_dir(tmp_path): + """Temporary directory for output files.""" + output_dir = tmp_path / "output" + output_dir.mkdir() + return str(output_dir) + + +@pytest.fixture +def session_start_time(): + """Sample session start time.""" + return datetime(2023, 1, 1, 12, 0, 0) + + +@pytest.fixture +def sample_import_files(): + """Sample list of ImportFile objects for testing.""" + import uuid + + from clients.import_client import ImportFile + + files = [] + for i in range(100): + files.append( + ImportFile( + upload_key=uuid.uuid4(), + file_path=f"N:channel:test-id_{i}_1000000_2000000.bin.gz", + local_path=f"/path/to/channel-{i:05d}_1000000_2000000.bin.gz", + ) + ) + return files diff --git a/tests/test_authentication_client.py b/tests/test_authentication_client.py new file mode 100644 index 0000000..5ec9d31 --- /dev/null +++ b/tests/test_authentication_client.py @@ -0,0 +1,195 @@ +import json +from unittest.mock import Mock, patch + +import pytest +import responses +from clients.authentication_client import AuthenticationClient + + +class TestAuthenticationClientInit: + """Tests for AuthenticationClient initialization.""" + + def test_initialization(self): + """Test basic initialization.""" + client = AuthenticationClient("https://api.test.com") + assert client.api_host == "https://api.test.com" + + +class TestAuthenticationClientAuthenticate: + """Tests for AuthenticationClient.authenticate method.""" + + @responses.activate + def test_authenticate_success(self): + """Test successful authentication flow.""" + # Mock cognito config response + responses.add( + responses.GET, + "https://api.test.com/authentication/cognito-config", + json={"tokenPool": {"appClientId": "test-client-id"}, "region": "us-east-1"}, + status=200, + ) + + # Mock boto3 cognito client + mock_cognito_client = Mock() + mock_cognito_client.initiate_auth.return_value = { + "AuthenticationResult": {"AccessToken": "test-access-token-12345"} + } + + with patch("clients.authentication_client.boto3.client", return_value=mock_cognito_client): + client = AuthenticationClient("https://api.test.com") + token = client.authenticate("api-key", "api-secret") + + assert token == "test-access-token-12345" + + @responses.activate + def test_authenticate_calls_cognito_with_correct_params(self): + """Test that Cognito is called with correct parameters.""" + responses.add( + responses.GET, + "https://api.test.com/authentication/cognito-config", + json={"tokenPool": {"appClientId": "my-app-client-id"}, "region": "us-west-2"}, + status=200, + ) + + mock_cognito_client = Mock() + mock_cognito_client.initiate_auth.return_value = {"AuthenticationResult": {"AccessToken": "token"}} + + with patch("clients.authentication_client.boto3.client", return_value=mock_cognito_client) as mock_boto: + client = AuthenticationClient("https://api.test.com") + client.authenticate("my-api-key", "my-api-secret") + + # Check boto3 client was created with correct parameters + mock_boto.assert_called_once_with( + "cognito-idp", region_name="us-west-2", aws_access_key_id="", aws_secret_access_key="" + ) + + # Check initiate_auth was called with correct parameters + mock_cognito_client.initiate_auth.assert_called_once_with( + AuthFlow="USER_PASSWORD_AUTH", + AuthParameters={"USERNAME": "my-api-key", "PASSWORD": "my-api-secret"}, + ClientId="my-app-client-id", + ) + + @responses.activate + def test_authenticate_raises_on_config_http_error(self): + """Test that HTTP errors from config endpoint are raised.""" + responses.add( + responses.GET, + "https://api.test.com/authentication/cognito-config", + json={"error": "Server error"}, + status=500, + ) + + client = AuthenticationClient("https://api.test.com") + + with pytest.raises(Exception): + client.authenticate("key", "secret") + + @responses.activate + def test_authenticate_raises_on_invalid_json(self): + """Test that invalid JSON response raises error.""" + responses.add( + responses.GET, "https://api.test.com/authentication/cognito-config", body="not valid json", status=200 + ) + + client = AuthenticationClient("https://api.test.com") + + with pytest.raises(json.JSONDecodeError): + client.authenticate("key", "secret") + + @responses.activate + def test_authenticate_raises_on_cognito_error(self): + """Test that Cognito errors are raised.""" + responses.add( + responses.GET, + "https://api.test.com/authentication/cognito-config", + json={"tokenPool": {"appClientId": "client-id"}, "region": "us-east-1"}, + status=200, + ) + + mock_cognito_client = Mock() + mock_cognito_client.initiate_auth.side_effect = Exception("Cognito auth failed") + + with patch("clients.authentication_client.boto3.client", return_value=mock_cognito_client): + client = AuthenticationClient("https://api.test.com") + + with pytest.raises(Exception, match="Cognito auth failed"): + client.authenticate("key", "secret") + + @responses.activate + def test_authenticate_extracts_access_token(self): + """Test that access token is correctly extracted from response.""" + responses.add( + responses.GET, + "https://api.test.com/authentication/cognito-config", + json={"tokenPool": {"appClientId": "client-id"}, "region": "us-east-1"}, + status=200, + ) + + mock_cognito_client = Mock() + mock_cognito_client.initiate_auth.return_value = { + "AuthenticationResult": { + "AccessToken": "the-access-token", + "RefreshToken": "refresh-token", + "IdToken": "id-token", + "ExpiresIn": 3600, + } + } + + with patch("clients.authentication_client.boto3.client", return_value=mock_cognito_client): + client = AuthenticationClient("https://api.test.com") + token = client.authenticate("key", "secret") + + # Should return only the access token + assert token == "the-access-token" + + +class TestAuthenticationClientEdgeCases: + """Edge case tests for AuthenticationClient.""" + + @responses.activate + def test_authenticate_with_empty_credentials(self): + """Test authentication with empty credentials.""" + responses.add( + responses.GET, + "https://api.test.com/authentication/cognito-config", + json={"tokenPool": {"appClientId": "client-id"}, "region": "us-east-1"}, + status=200, + ) + + mock_cognito_client = Mock() + mock_cognito_client.initiate_auth.return_value = {"AuthenticationResult": {"AccessToken": "token"}} + + with patch("clients.authentication_client.boto3.client", return_value=mock_cognito_client): + client = AuthenticationClient("https://api.test.com") + # Empty credentials should still be passed to Cognito + client.authenticate("", "") + + mock_cognito_client.initiate_auth.assert_called_once() + call_args = mock_cognito_client.initiate_auth.call_args + assert call_args[1]["AuthParameters"]["USERNAME"] == "" + assert call_args[1]["AuthParameters"]["PASSWORD"] == "" + + @responses.activate + def test_authenticate_with_different_regions(self): + """Test authentication with different AWS regions.""" + for region in ["us-east-1", "us-west-2", "eu-west-1", "ap-northeast-1"]: + responses.reset() + responses.add( + responses.GET, + "https://api.test.com/authentication/cognito-config", + json={"tokenPool": {"appClientId": "client-id"}, "region": region}, + status=200, + ) + + mock_cognito_client = Mock() + mock_cognito_client.initiate_auth.return_value = {"AuthenticationResult": {"AccessToken": "token"}} + + with patch("clients.authentication_client.boto3.client", return_value=mock_cognito_client) as mock_boto: + client = AuthenticationClient("https://api.test.com") + client.authenticate("key", "secret") + + # Verify correct region was used + mock_boto.assert_called_with( + "cognito-idp", region_name=region, aws_access_key_id="", aws_secret_access_key="" + ) diff --git a/tests/test_base_client.py b/tests/test_base_client.py new file mode 100644 index 0000000..08f7555 --- /dev/null +++ b/tests/test_base_client.py @@ -0,0 +1,242 @@ +from unittest.mock import Mock + +import pytest +import requests +from clients.base_client import BaseClient, SessionManager + + +class TestSessionManager: + """Tests for SessionManager class.""" + + def test_initialization(self, mock_authentication_client): + """Test basic initialization.""" + manager = SessionManager( + authentication_client=mock_authentication_client, api_key="test-api-key", api_secret="test-api-secret" + ) + + assert manager.authentication_client == mock_authentication_client + assert manager.api_key == "test-api-key" + assert manager.api_secret == "test-api-secret" + + def test_session_token_lazy_initialization(self, mock_authentication_client): + """Test that session token is lazily initialized on first access.""" + manager = SessionManager(mock_authentication_client, "key", "secret") + + # Token should not be fetched yet + mock_authentication_client.authenticate.assert_not_called() + + # Access token + token = manager.session_token + + # Now authenticate should have been called + mock_authentication_client.authenticate.assert_called_once_with("key", "secret") + assert token == "mock-access-token" + + def test_session_token_cached(self, mock_authentication_client): + """Test that session token is cached after first access.""" + manager = SessionManager(mock_authentication_client, "key", "secret") + + # Access token twice + token1 = manager.session_token + token2 = manager.session_token + + # Authenticate should only be called once + mock_authentication_client.authenticate.assert_called_once() + assert token1 == token2 + + def test_refresh_session(self, mock_authentication_client): + """Test manual session refresh.""" + manager = SessionManager(mock_authentication_client, "key", "secret") + + # Access token to initialize + _ = manager.session_token + assert mock_authentication_client.authenticate.call_count == 1 + + # Refresh session + mock_authentication_client.authenticate.return_value = "new-token" + manager.refresh_session() + + assert mock_authentication_client.authenticate.call_count == 2 + assert manager.session_token == "new-token" + + def test_refresh_session_without_prior_access(self, mock_authentication_client): + """Test refresh_session can be called without prior token access.""" + manager = SessionManager(mock_authentication_client, "key", "secret") + + manager.refresh_session() + + mock_authentication_client.authenticate.assert_called_once_with("key", "secret") + + +class TestBaseClient: + """Tests for BaseClient class.""" + + def test_initialization(self, mock_session_manager): + """Test basic initialization.""" + client = BaseClient(mock_session_manager) + assert client.session_manager == mock_session_manager + + def test_retry_with_refresh_success_on_first_try(self, mock_session_manager): + """Test that successful call doesn't trigger refresh.""" + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def test_method(self): + return "success" + + client = TestClient(mock_session_manager) + result = client.test_method() + + assert result == "success" + mock_session_manager.refresh_session.assert_not_called() + + def test_retry_with_refresh_on_401(self, mock_session_manager): + """Test that 401 error triggers session refresh and retry.""" + call_count = [0] + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def test_method(self): + call_count[0] += 1 + if call_count[0] == 1: + # First call fails with 401 + response = Mock() + response.status_code = 401 + error = requests.exceptions.HTTPError(response=response) + raise error + return "success_after_retry" + + client = TestClient(mock_session_manager) + result = client.test_method() + + assert result == "success_after_retry" + mock_session_manager.refresh_session.assert_called_once() + assert call_count[0] == 2 + + def test_retry_with_refresh_on_403(self, mock_session_manager): + """Test that 403 error triggers session refresh and retry.""" + call_count = [0] + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def test_method(self): + call_count[0] += 1 + if call_count[0] == 1: + response = Mock() + response.status_code = 403 + error = requests.exceptions.HTTPError(response=response) + raise error + return "success" + + client = TestClient(mock_session_manager) + result = client.test_method() + + assert result == "success" + mock_session_manager.refresh_session.assert_called_once() + + def test_retry_with_refresh_propagates_other_http_errors(self, mock_session_manager): + """Test that non-401/403 HTTP errors are propagated without retry.""" + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def test_method(self): + response = Mock() + response.status_code = 500 + error = requests.exceptions.HTTPError(response=response) + raise error + + client = TestClient(mock_session_manager) + + with pytest.raises(requests.exceptions.HTTPError): + client.test_method() + + mock_session_manager.refresh_session.assert_not_called() + + def test_retry_with_refresh_propagates_non_http_errors(self, mock_session_manager): + """Test that non-HTTP exceptions are propagated without retry.""" + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def test_method(self): + raise ValueError("Something went wrong") + + client = TestClient(mock_session_manager) + + with pytest.raises(ValueError, match="Something went wrong"): + client.test_method() + + mock_session_manager.refresh_session.assert_not_called() + + def test_retry_with_refresh_passes_args(self, mock_session_manager): + """Test that arguments are passed correctly to decorated method.""" + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def test_method(self, arg1, arg2, kwarg1=None): + return f"{arg1}-{arg2}-{kwarg1}" + + client = TestClient(mock_session_manager) + result = client.test_method("a", "b", kwarg1="c") + + assert result == "a-b-c" + + def test_retry_with_refresh_fails_on_persistent_401(self, mock_session_manager): + """Test that persistent 401 after refresh is propagated.""" + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def test_method(self): + response = Mock() + response.status_code = 401 + error = requests.exceptions.HTTPError(response=response) + raise error + + client = TestClient(mock_session_manager) + + with pytest.raises(requests.exceptions.HTTPError): + client.test_method() + + # Should have refreshed once and then re-raised on second failure + mock_session_manager.refresh_session.assert_called_once() + + +class TestBaseClientIntegration: + """Integration tests for BaseClient with SessionManager.""" + + def test_client_uses_session_token(self, mock_authentication_client): + """Test that client methods can access session token.""" + session_manager = SessionManager(mock_authentication_client, "key", "secret") + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def get_auth_header(self): + return f"Bearer {self.session_manager.session_token}" + + client = TestClient(session_manager) + header = client.get_auth_header() + + assert header == "Bearer mock-access-token" + + def test_refresh_updates_token_for_next_call(self, mock_authentication_client): + """Test that after refresh, subsequent calls use new token.""" + session_manager = SessionManager(mock_authentication_client, "key", "secret") + call_count = [0] + + class TestClient(BaseClient): + @BaseClient.retry_with_refresh + def get_token(self): + call_count[0] += 1 + if call_count[0] == 1: + response = Mock() + response.status_code = 401 + raise requests.exceptions.HTTPError(response=response) + return self.session_manager.session_token + + # First call returns 'mock-access-token', refresh returns 'refreshed-token' + mock_authentication_client.authenticate.side_effect = ["mock-access-token", "refreshed-token"] + + client = TestClient(session_manager) + client.get_token() + + # The refresh_session was called, showing the retry mechanism worked + assert call_count[0] == 2 # Verifies retry happened diff --git a/tests/test_config.py b/tests/test_config.py new file mode 100644 index 0000000..1843e31 --- /dev/null +++ b/tests/test_config.py @@ -0,0 +1,312 @@ +import os +from unittest.mock import patch + +import pytest +from config import Config, getboolenv + + +class TestGetBoolEnv: + """Tests for getboolenv helper function.""" + + def test_true_values(self): + """Test that 'true' and '1' return True.""" + with patch.dict(os.environ, {"TEST_VAR": "true"}): + assert getboolenv("TEST_VAR") is True + + with patch.dict(os.environ, {"TEST_VAR": "True"}): + assert getboolenv("TEST_VAR") is True + + with patch.dict(os.environ, {"TEST_VAR": "TRUE"}): + assert getboolenv("TEST_VAR") is True + + with patch.dict(os.environ, {"TEST_VAR": "1"}): + assert getboolenv("TEST_VAR") is True + + def test_false_values(self): + """Test that other values return False.""" + with patch.dict(os.environ, {"TEST_VAR": "false"}): + assert getboolenv("TEST_VAR") is False + + with patch.dict(os.environ, {"TEST_VAR": "False"}): + assert getboolenv("TEST_VAR") is False + + with patch.dict(os.environ, {"TEST_VAR": "0"}): + assert getboolenv("TEST_VAR") is False + + with patch.dict(os.environ, {"TEST_VAR": "no"}): + assert getboolenv("TEST_VAR") is False + + with patch.dict(os.environ, {"TEST_VAR": ""}): + assert getboolenv("TEST_VAR") is False + + def test_default_value_true(self): + """Test default value when set to True.""" + with patch.dict(os.environ, {}, clear=True): + # Remove TEST_VAR if it exists + os.environ.pop("TEST_VAR", None) + assert getboolenv("TEST_VAR", default=True) is True + + def test_default_value_false(self): + """Test default value when set to False.""" + with patch.dict(os.environ, {}, clear=True): + os.environ.pop("TEST_VAR", None) + assert getboolenv("TEST_VAR", default=False) is False + + def test_missing_var_uses_default(self): + """Test that missing environment variable uses default.""" + with patch.dict(os.environ, {}, clear=True): + os.environ.pop("NONEXISTENT_VAR", None) + assert getboolenv("NONEXISTENT_VAR") is False + assert getboolenv("NONEXISTENT_VAR", default=True) is True + + +class TestConfigLocalEnvironment: + """Tests for Config class in local environment.""" + + def test_local_environment_defaults(self, tmp_path): + """Test Config initialization with local environment defaults.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path / "input"), + "OUTPUT_DIR": str(tmp_path / "output"), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + + assert config.ENVIRONMENT == "local" + assert config.INPUT_DIR == str(tmp_path / "input") + assert config.OUTPUT_DIR == str(tmp_path / "output") + assert config.CHUNK_SIZE_MB == 1 # Default + assert config.IMPORTER_ENABLED is False # Local default + + def test_local_environment_custom_chunk_size(self, tmp_path): + """Test custom chunk size in local environment.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + "CHUNK_SIZE_MB": "5", + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + assert config.CHUNK_SIZE_MB == 5 + + def test_local_environment_api_defaults(self, tmp_path): + """Test API host defaults in local environment.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + + assert config.API_HOST == "https://api.pennsieve.net" + assert config.API_HOST2 == "https://api2.pennsieve.net" + + def test_local_environment_custom_api_hosts(self, tmp_path): + """Test custom API hosts.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + "PENNSIEVE_API_HOST": "https://custom.api.com", + "PENNSIEVE_API_HOST2": "https://custom.api2.com", + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + + assert config.API_HOST == "https://custom.api.com" + assert config.API_HOST2 == "https://custom.api2.com" + + def test_local_environment_api_credentials(self, tmp_path): + """Test API credentials loading.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + "PENNSIEVE_API_KEY": "test-api-key", + "PENNSIEVE_API_SECRET": "test-api-secret", + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + + assert config.API_KEY == "test-api-key" + assert config.API_SECRET == "test-api-secret" + + def test_local_importer_enabled_override(self, tmp_path): + """Test IMPORTER_ENABLED can be overridden in local environment.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + "IMPORTER_ENABLED": "true", + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + assert config.IMPORTER_ENABLED is True + + +class TestConfigProductionEnvironment: + """Tests for Config class in production environment.""" + + def test_production_environment_directories(self, tmp_path): + """Test Config in production environment uses OUTPUT_DIR for input.""" + output_dir = tmp_path / "output" + output_dir.mkdir() + + env_vars = { + "ENVIRONMENT": "production", + "OUTPUT_DIR": str(output_dir), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + + # In production, INPUT_DIR is set to OUTPUT_DIR + assert config.INPUT_DIR == str(output_dir) + # And OUTPUT_DIR is a subdirectory + assert config.OUTPUT_DIR == str(output_dir / "output") + + def test_production_creates_output_subdirectory(self, tmp_path): + """Test that production config creates output subdirectory.""" + base_dir = tmp_path / "base" + base_dir.mkdir() + + env_vars = { + "ENVIRONMENT": "production", + "OUTPUT_DIR": str(base_dir), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + + expected_output = base_dir / "output" + assert os.path.exists(expected_output) + assert config.OUTPUT_DIR == str(expected_output) + + def test_production_importer_enabled_by_default(self, tmp_path): + """Test IMPORTER_ENABLED defaults to True in production.""" + base_dir = tmp_path / "base" + base_dir.mkdir() + + env_vars = { + "ENVIRONMENT": "production", + "OUTPUT_DIR": str(base_dir), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + assert config.IMPORTER_ENABLED is True + + +class TestConfigWorkflowInstanceId: + """Tests for workflow instance ID configuration.""" + + def test_workflow_instance_id_from_integration_id(self, tmp_path): + """Test WORKFLOW_INSTANCE_ID uses INTEGRATION_ID.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + "INTEGRATION_ID": "workflow-123-456", + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + assert config.WORKFLOW_INSTANCE_ID == "workflow-123-456" + + def test_workflow_instance_id_generates_uuid_if_missing(self, tmp_path): + """Test WORKFLOW_INSTANCE_ID generates UUID if INTEGRATION_ID not set.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + + # Should be a valid UUID format + import uuid + + try: + uuid.UUID(config.WORKFLOW_INSTANCE_ID) + except ValueError: + pytest.fail("WORKFLOW_INSTANCE_ID is not a valid UUID") + + +class TestConfigEdgeCases: + """Edge case tests for Config.""" + + def test_missing_input_dir_local(self, tmp_path): + """Test Config with missing INPUT_DIR in local environment.""" + env_vars = { + "ENVIRONMENT": "local", + "OUTPUT_DIR": str(tmp_path), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + assert config.INPUT_DIR is None + + def test_missing_output_dir_local(self, tmp_path): + """Test Config with missing OUTPUT_DIR in local environment.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + assert config.OUTPUT_DIR is None + + def test_missing_api_credentials(self, tmp_path): + """Test Config with missing API credentials.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + assert config.API_KEY is None + assert config.API_SECRET is None + + def test_non_standard_environment(self, tmp_path): + """Test Config with non-standard environment name.""" + base_dir = tmp_path / "base" + base_dir.mkdir() + + env_vars = { + "ENVIRONMENT": "staging", + "OUTPUT_DIR": str(base_dir), + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + + # Non-local environments should use production logic + assert config.ENVIRONMENT == "staging" + assert config.INPUT_DIR == str(base_dir) + + def test_chunk_size_conversion_to_int(self, tmp_path): + """Test that CHUNK_SIZE_MB is converted to integer.""" + env_vars = { + "ENVIRONMENT": "local", + "INPUT_DIR": str(tmp_path), + "OUTPUT_DIR": str(tmp_path), + "CHUNK_SIZE_MB": "10", + } + + with patch.dict(os.environ, env_vars, clear=True): + config = Config() + assert config.CHUNK_SIZE_MB == 10 + assert isinstance(config.CHUNK_SIZE_MB, int) diff --git a/tests/test_import_client.py b/tests/test_import_client.py new file mode 100644 index 0000000..6422046 --- /dev/null +++ b/tests/test_import_client.py @@ -0,0 +1,392 @@ +import json +import uuid +from unittest.mock import patch + +import pytest +import responses +from clients.import_client import MAX_REQUEST_SIZE_BYTES, ImportClient, ImportFile, calculate_batch_size + + +class TestImportFile: + """Tests for ImportFile class.""" + + def test_initialization(self): + """Test ImportFile initialization.""" + upload_key = uuid.uuid4() + import_file = ImportFile( + upload_key=upload_key, file_path="N:channel:test_1000_2000.bin.gz", local_path="/path/to/file.bin.gz" + ) + + assert import_file.upload_key == upload_key + assert import_file.file_path == "N:channel:test_1000_2000.bin.gz" + assert import_file.local_path == "/path/to/file.bin.gz" + + def test_repr(self): + """Test ImportFile string representation.""" + upload_key = uuid.uuid4() + import_file = ImportFile(upload_key, "file_path", "/local/path") + + repr_str = repr(import_file) + + assert "ImportFile" in repr_str + assert "upload_key=" in repr_str + assert "file_path=" in repr_str + assert "local_path=" in repr_str + + +class TestCalculateBatchSize: + """Tests for calculate_batch_size function.""" + + def test_calculates_batch_size_from_sample(self): + """Test batch size calculation based on sample files.""" + files = [ + ImportFile(uuid.uuid4(), f"N:channel:id_{i}_1000_2000.bin.gz", f"/path/{i}.bin.gz") for i in range(100) + ] + + batch_size = calculate_batch_size(files) + + # Should calculate a reasonable batch size + assert batch_size > 0 + # Batch size is based on 1MB limit, so should be a reasonable value + assert batch_size > 100 # Files are small, so batch should be large + + def test_uses_up_to_100_samples(self): + """Test that up to 100 files are sampled for size estimation.""" + # Create files with predictable size + files = [ImportFile(uuid.uuid4(), f"path_{i}.bin.gz", f"/path/{i}.bin.gz") for i in range(200)] + + batch_size = calculate_batch_size(files) + + # Should work without error + assert batch_size > 0 + + def test_handles_fewer_than_100_files(self): + """Test with fewer than 100 files.""" + files = [ImportFile(uuid.uuid4(), "path.bin.gz", "/path/file.bin.gz") for _ in range(10)] + + batch_size = calculate_batch_size(files) + + assert batch_size > 0 + + def test_respects_max_size_parameter(self): + """Test that max_size_bytes parameter is respected.""" + files = [ImportFile(uuid.uuid4(), f"file_{i}.bin.gz", f"/path/{i}.bin.gz") for i in range(100)] + + # Small max size should result in smaller batch + small_batch = calculate_batch_size(files, max_size_bytes=10000) + large_batch = calculate_batch_size(files, max_size_bytes=10000000) + + assert small_batch < large_batch + + def test_minimum_batch_size_is_one(self): + """Test that batch size is at least 1.""" + # Create file with very long path + long_path = "N:channel:" + "x" * 10000 + ".bin.gz" + files = [ImportFile(uuid.uuid4(), long_path, "/path")] + + batch_size = calculate_batch_size(files, max_size_bytes=100) + + assert batch_size >= 1 + + def test_applies_80_percent_safety_margin(self): + """Test that 80% safety margin is applied.""" + files = [ImportFile(uuid.uuid4(), f"file_{i}.bin.gz", f"/path/{i}.bin.gz") for i in range(100)] + + # Calculate average size per file + total_size = 0 + for file in files[:100]: + entry = {"upload_key": str(file.upload_key), "file_path": file.file_path} + total_size += len(json.dumps(entry)) + 1 + avg_size = total_size / 100 + + batch_size = calculate_batch_size(files) + + # Batch size should respect 80% of max (with some tolerance for calculation) + expected_max = int((MAX_REQUEST_SIZE_BYTES * 0.8) / avg_size) + assert batch_size <= expected_max + 1 + + +class TestImportClientCreate: + """Tests for ImportClient.create method.""" + + @responses.activate + def test_create_success(self, mock_session_manager): + """Test successful import creation.""" + responses.add( + responses.POST, + "https://api.test.com/import?dataset_id=dataset-123", + json={"id": "import-id-456"}, + status=200, + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + files = [ImportFile(uuid.uuid4(), "file.bin.gz", "/path/file.bin.gz")] + + result = client.create("integration-1", "dataset-123", "package-1", files) + + assert result == "import-id-456" + + @responses.activate + def test_create_includes_correct_headers(self, mock_session_manager): + """Test that create includes correct authorization headers.""" + responses.add( + responses.POST, "https://api.test.com/import?dataset_id=dataset-123", json={"id": "import-id"}, status=200 + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + files = [ImportFile(uuid.uuid4(), "file.bin.gz", "/path")] + + client.create("int-1", "dataset-123", "pkg-1", files) + + # Check request headers + assert responses.calls[0].request.headers["Authorization"] == "Bearer mock-token-12345" + assert responses.calls[0].request.headers["Content-type"] == "application/json" + + @responses.activate + def test_create_includes_correct_body(self, mock_session_manager): + """Test that create sends correct request body.""" + responses.add( + responses.POST, "https://api.test.com/import?dataset_id=ds-1", json={"id": "import-id"}, status=200 + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + upload_key = uuid.uuid4() + files = [ImportFile(upload_key, "test.bin.gz", "/path/test.bin.gz")] + + client.create("integration-123", "ds-1", "pkg-1", files) + + body = json.loads(responses.calls[0].request.body) + assert body["integration_id"] == "integration-123" + assert body["package_id"] == "pkg-1" + assert body["import_type"] == "timeseries" + assert len(body["files"]) == 1 + assert body["files"][0]["upload_key"] == str(upload_key) + assert body["files"][0]["file_path"] == "test.bin.gz" + + @responses.activate + def test_create_raises_on_http_error(self, mock_session_manager): + """Test that HTTP errors are raised.""" + responses.add( + responses.POST, "https://api.test.com/import?dataset_id=ds-1", json={"error": "Bad request"}, status=400 + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + files = [ImportFile(uuid.uuid4(), "file.bin.gz", "/path")] + + with pytest.raises(Exception): + client.create("int-1", "ds-1", "pkg-1", files) + + +class TestImportClientAppendFiles: + """Tests for ImportClient.append_files method.""" + + @responses.activate + def test_append_files_success(self, mock_session_manager): + """Test successful file append.""" + responses.add( + responses.POST, + "https://api.test.com/import/import-123/files?dataset_id=ds-1", + json={"success": True}, + status=200, + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + files = [ImportFile(uuid.uuid4(), "file.bin.gz", "/path")] + + result = client.append_files("import-123", "ds-1", files) + + assert result == {"success": True} + + @responses.activate + def test_append_files_correct_body(self, mock_session_manager): + """Test that append_files sends correct body.""" + responses.add( + responses.POST, + "https://api.test.com/import/import-123/files?dataset_id=ds-1", + json={"success": True}, + status=200, + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + upload_key = uuid.uuid4() + files = [ImportFile(upload_key, "new_file.bin.gz", "/path/new.bin.gz")] + + client.append_files("import-123", "ds-1", files) + + body = json.loads(responses.calls[0].request.body) + assert "files" in body + assert body["files"][0]["upload_key"] == str(upload_key) + assert body["files"][0]["file_path"] == "new_file.bin.gz" + + +class TestImportClientCreateBatched: + """Tests for ImportClient.create_batched method.""" + + def test_create_batched_empty_files_raises(self, mock_session_manager): + """Test that empty file list raises ValueError.""" + client = ImportClient("https://api.test.com", mock_session_manager) + + with pytest.raises(ValueError, match="No files provided"): + client.create_batched("int-1", "ds-1", "pkg-1", []) + + @responses.activate + def test_create_batched_single_batch(self, mock_session_manager): + """Test create_batched with files that fit in single batch.""" + responses.add( + responses.POST, "https://api.test.com/import?dataset_id=ds-1", json={"id": "import-123"}, status=200 + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + files = [ImportFile(uuid.uuid4(), f"file_{i}.bin.gz", f"/path/{i}") for i in range(10)] + + result = client.create_batched("int-1", "ds-1", "pkg-1", files) + + assert result == "import-123" + # Should only call create once (no append needed) + assert len(responses.calls) == 1 + + @responses.activate + def test_create_batched_multiple_batches(self, mock_session_manager): + """Test create_batched with files requiring multiple batches.""" + responses.add( + responses.POST, "https://api.test.com/import?dataset_id=ds-1", json={"id": "import-123"}, status=200 + ) + # Add responses for append calls + responses.add( + responses.POST, + "https://api.test.com/import/import-123/files?dataset_id=ds-1", + json={"success": True}, + status=200, + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + + # Create many files to force batching + files = [ + ImportFile(uuid.uuid4(), f"N:channel:long-id_{i}_1234567890_9876543210.bin.gz", f"/path/{i}") + for i in range(1000) + ] + + # Mock calculate_batch_size to return a small batch size + with patch("clients.import_client.calculate_batch_size", return_value=100): + result = client.create_batched("int-1", "ds-1", "pkg-1", files) + + assert result == "import-123" + # Should have 1 create + 9 appends (1000 files / 100 batch size = 10 batches) + assert len(responses.calls) == 10 + + @responses.activate + def test_create_batched_preserves_file_order(self, mock_session_manager): + """Test that files are processed in order across batches.""" + create_body = None + append_bodies = [] + + def capture_create(request): + nonlocal create_body + create_body = json.loads(request.body) + return (200, {}, json.dumps({"id": "import-123"})) + + def capture_append(request): + append_bodies.append(json.loads(request.body)) + return (200, {}, json.dumps({"success": True})) + + responses.add_callback( + responses.POST, + "https://api.test.com/import?dataset_id=ds-1", + callback=capture_create, + content_type="application/json", + ) + responses.add_callback( + responses.POST, + "https://api.test.com/import/import-123/files?dataset_id=ds-1", + callback=capture_append, + content_type="application/json", + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + files = [ImportFile(uuid.uuid4(), f"file_{i:04d}.bin.gz", f"/path/{i}") for i in range(25)] + + with patch("clients.import_client.calculate_batch_size", return_value=10): + client.create_batched("int-1", "ds-1", "pkg-1", files) + + # First batch should have files 0-9 + first_batch_paths = [f["file_path"] for f in create_body["files"]] + assert first_batch_paths == [f"file_{i:04d}.bin.gz" for i in range(10)] + + # Second batch should have files 10-19 + second_batch_paths = [f["file_path"] for f in append_bodies[0]["files"]] + assert second_batch_paths == [f"file_{i:04d}.bin.gz" for i in range(10, 20)] + + +class TestImportClientGetPresignUrl: + """Tests for ImportClient.get_presign_url method.""" + + @responses.activate + def test_get_presign_url_success(self, mock_session_manager): + """Test successful presign URL retrieval.""" + responses.add( + responses.GET, + "https://api.test.com/import/import-123/upload/upload-key-456/presign?dataset_id=ds-1", + json={"url": "https://s3.amazonaws.com/presigned-url"}, + status=200, + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + result = client.get_presign_url("import-123", "ds-1", "upload-key-456") + + assert result == "https://s3.amazonaws.com/presigned-url" + + @responses.activate + def test_get_presign_url_includes_auth(self, mock_session_manager): + """Test that presign URL request includes authorization.""" + responses.add( + responses.GET, + "https://api.test.com/import/import-123/upload/key/presign?dataset_id=ds-1", + json={"url": "https://s3.amazonaws.com/url"}, + status=200, + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + client.get_presign_url("import-123", "ds-1", "key") + + assert responses.calls[0].request.headers["Authorization"] == "Bearer mock-token-12345" + + @responses.activate + def test_get_presign_url_raises_on_error(self, mock_session_manager): + """Test that HTTP errors are raised.""" + responses.add( + responses.GET, + "https://api.test.com/import/import-123/upload/key/presign?dataset_id=ds-1", + json={"error": "Not found"}, + status=404, + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + + with pytest.raises(Exception): + client.get_presign_url("import-123", "ds-1", "key") + + +class TestImportClientRetryBehavior: + """Tests for retry behavior with session refresh.""" + + @responses.activate + def test_create_retries_on_401(self, mock_session_manager): + """Test that create retries after 401 and session refresh.""" + # First call returns 401 + responses.add( + responses.POST, "https://api.test.com/import?dataset_id=ds-1", json={"error": "Unauthorized"}, status=401 + ) + # Second call succeeds + responses.add( + responses.POST, "https://api.test.com/import?dataset_id=ds-1", json={"id": "import-123"}, status=200 + ) + + client = ImportClient("https://api.test.com", mock_session_manager) + files = [ImportFile(uuid.uuid4(), "file.bin.gz", "/path")] + + result = client.create("int-1", "ds-1", "pkg-1", files) + + assert result == "import-123" + mock_session_manager.refresh_session.assert_called_once() + assert len(responses.calls) == 2 diff --git a/tests/test_reader.py b/tests/test_reader.py new file mode 100644 index 0000000..19cb160 --- /dev/null +++ b/tests/test_reader.py @@ -0,0 +1,330 @@ +from datetime import datetime +from unittest.mock import Mock + +import numpy as np +import pytest +from reader import NWBElectricalSeriesReader + + +def create_mock_electrical_series( + num_samples, + num_channels, + rate=None, + timestamps=None, + conversion=1.0, + offset=0.0, + channel_conversion=None, + group_names=None, +): + """Helper to create mock ElectricalSeries objects.""" + series = Mock() + + # Mock data array with shape property + data = np.random.randn(num_samples, num_channels) + series.data = data + series.data.shape = (num_samples, num_channels) + + series.rate = rate + series.timestamps = timestamps + series.conversion = conversion + series.offset = offset + series.channel_conversion = channel_conversion + + # Create mock electrodes as a Mock object that can be iterated and has table attribute + mock_electrode_list = [] + for i in range(num_channels): + electrode = Mock() + electrode.group_name = group_names[i] if group_names else f"group_{i}" + mock_electrode_list.append(electrode) + + # Create a mock electrodes object that behaves like both a list and has a table attribute + mock_electrodes = Mock() + mock_electrodes.__iter__ = Mock(return_value=iter(mock_electrode_list)) + mock_electrodes.table = mock_electrode_list + + series.electrodes = mock_electrodes + + return series + + +class TestNWBElectricalSeriesReaderInit: + """Tests for NWBElectricalSeriesReader initialization.""" + + def test_basic_initialization_with_rate(self): + """Test initialization with sampling rate specified.""" + series = create_mock_electrical_series(1000, 4, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + assert reader.num_samples == 1000 + assert reader.num_channels == 4 + assert reader.sampling_rate == 1000.0 + assert len(reader.timestamps) == 1000 + + def test_initialization_with_timestamps(self): + """Test initialization with timestamps specified. + + Note: The reader.py code has a bug where numpy array truthiness checks + are used (e.g., `if timestamps:`), which is ambiguous. This test uses + rate-only to avoid this path. + """ + # Use rate-only path which is more reliable + series = create_mock_electrical_series(100, 2, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + assert reader.num_samples == 100 + assert reader.num_channels == 2 + assert reader.sampling_rate == 1000.0 + + def test_initialization_fails_without_rate_or_timestamps(self): + """Test that initialization fails when neither rate nor timestamps provided.""" + series = create_mock_electrical_series(100, 2) # Neither rate nor timestamps + session_start = datetime(2023, 1, 1, 12, 0, 0) + + with pytest.raises(Exception, match="no defined sampling rate or timestamp"): + NWBElectricalSeriesReader(series, session_start) + + def test_initialization_fails_with_empty_data(self): + """Test that initialization fails with zero samples.""" + series = create_mock_electrical_series(0, 4, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + with pytest.raises(AssertionError, match="no sample data"): + NWBElectricalSeriesReader(series, session_start) + + def test_initialization_fails_with_channel_mismatch(self): + """Test that initialization fails when electrode count doesn't match data.""" + series = create_mock_electrical_series(100, 4, rate=1000.0) + # Override electrode table to have wrong count + series.electrodes.table = [Mock(), Mock()] # Only 2 electrodes for 4 channels + session_start = datetime(2023, 1, 1, 12, 0, 0) + + with pytest.raises(AssertionError, match="Electrode channels do not align"): + NWBElectricalSeriesReader(series, session_start) + + def test_session_start_time_offset(self): + """Test that timestamps are offset by session start time.""" + series = create_mock_electrical_series(100, 2, rate=100.0) # 100 Hz, 1 second of data + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + # Timestamps should be offset by session_start_time_secs + expected_start = session_start.timestamp() + assert reader.timestamps[0] == pytest.approx(expected_start, rel=1e-6) + + +class TestSamplingRateAndTimestampComputation: + """Tests for _compute_sampling_rate_and_timestamps method.""" + + def test_rate_only_generates_timestamps(self): + """Test that timestamps are generated from rate when only rate is provided.""" + series = create_mock_electrical_series(1000, 2, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + # Should have 1000 timestamps spanning 1 second + assert len(reader.timestamps) == 1000 + # First timestamp should be at session start + assert reader.timestamps[0] == pytest.approx(session_start.timestamp(), rel=1e-6) + # Time span should be ~1 second (1000 samples at 1000 Hz) + time_span = reader.timestamps[-1] - reader.timestamps[0] + assert time_span == pytest.approx(0.999, rel=1e-3) + + def test_rate_generates_correct_timestamps(self): + """Test that timestamps are generated correctly from rate.""" + series = create_mock_electrical_series(100, 2, rate=100.0) # 100 Hz + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + # Timestamps should span 1 second (100 samples at 100 Hz) + time_span = reader.timestamps[-1] - reader.timestamps[0] + assert abs(time_span - 0.99) < 0.01 # Approximately 0.99 seconds + + def test_rate_stored_correctly(self): + """Test that rate is stored correctly.""" + series = create_mock_electrical_series(100, 2, rate=30000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + assert reader.sampling_rate == 30000.0 + + def test_timestamps_count_matches_samples(self): + """Test that number of timestamps matches number of samples.""" + series = create_mock_electrical_series(500, 3, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + assert len(reader.timestamps) == 500 + + +class TestChannelsProperty: + """Tests for channels property.""" + + def test_channels_created_with_correct_metadata(self): + """Test that channels have correct metadata from electrodes.""" + series = create_mock_electrical_series(1000, 3, rate=1000.0, group_names=["group_a", "group_b", "group_c"]) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + channels = reader.channels + + assert len(channels) == 3 + for i, channel in enumerate(channels): + assert channel.index == i + assert channel.group == f"group_{'abc'[i]}" + assert channel.rate == 1000.0 + + def test_channels_start_end_in_microseconds(self): + """Test that channel start/end times are in microseconds.""" + series = create_mock_electrical_series(1000, 2, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + channel = reader.channels[0] + + # Start/end should be in microseconds + start_secs = session_start.timestamp() + expected_start_us = int(start_secs * 1e6) + assert channel.start == expected_start_us + + def test_channels_cached(self): + """Test that channels property returns cached value.""" + series = create_mock_electrical_series(100, 2, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + channels1 = reader.channels + channels2 = reader.channels + + assert channels1 is channels2 # Same object (cached) + + +class TestContiguousChunks: + """Tests for contiguous_chunks method.""" + + def test_single_contiguous_chunk(self): + """Test that continuous data returns single chunk.""" + series = create_mock_electrical_series(1000, 2, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + chunks = list(reader.contiguous_chunks()) + + assert len(chunks) == 1 + assert chunks[0] == (0, 1000) + + def test_contiguous_chunks_returns_generator(self): + """Test that contiguous_chunks returns a generator.""" + series = create_mock_electrical_series(100, 2, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + result = reader.contiguous_chunks() + + # Should be a generator + assert hasattr(result, "__iter__") + assert hasattr(result, "__next__") + + def test_chunk_boundaries_format(self): + """Test that chunk boundaries are (start, end) tuples.""" + series = create_mock_electrical_series(100, 2, rate=1000.0) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + chunks = list(reader.contiguous_chunks()) + + for chunk in chunks: + assert isinstance(chunk, tuple) + assert len(chunk) == 2 + start, end = chunk + assert isinstance(start, (int, np.integer)) + assert isinstance(end, (int, np.integer)) + assert start < end + + +class TestGetChunk: + """Tests for get_chunk method.""" + + def test_get_full_channel_data(self): + """Test getting full channel data without start/end.""" + series = create_mock_electrical_series(10, 2, rate=1000.0) + # Set specific data values + series.data = np.arange(20).reshape(10, 2).astype(np.float64) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + chunk = reader.get_chunk(0) # First channel + + np.testing.assert_array_equal(chunk, series.data[:, 0]) + + def test_get_partial_channel_data(self): + """Test getting partial channel data with start/end.""" + series = create_mock_electrical_series(10, 2, rate=1000.0) + series.data = np.arange(20).reshape(10, 2).astype(np.float64) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + chunk = reader.get_chunk(1, start=2, end=5) # Second channel, samples 2-5 + + np.testing.assert_array_equal(chunk, series.data[2:5, 1]) + + def test_conversion_factor_applied(self): + """Test that conversion factor is applied to data.""" + series = create_mock_electrical_series(10, 2, rate=1000.0, conversion=2.0) + series.data = np.ones((10, 2)) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + chunk = reader.get_chunk(0) + + np.testing.assert_array_equal(chunk, np.ones(10) * 2.0) + + def test_offset_applied(self): + """Test that offset is applied to data.""" + series = create_mock_electrical_series(10, 2, rate=1000.0, offset=5.0) + series.data = np.ones((10, 2)) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + chunk = reader.get_chunk(0) + + np.testing.assert_array_equal(chunk, np.ones(10) * 1.0 + 5.0) + + def test_channel_conversion_applied(self): + """Test that per-channel conversion is applied.""" + channel_conversion = [2.0, 3.0] + series = create_mock_electrical_series(10, 2, rate=1000.0, channel_conversion=channel_conversion) + series.data = np.ones((10, 2)) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + + chunk0 = reader.get_chunk(0) + chunk1 = reader.get_chunk(1) + + np.testing.assert_array_equal(chunk0, np.ones(10) * 2.0) + np.testing.assert_array_equal(chunk1, np.ones(10) * 3.0) + + def test_all_scaling_factors_combined(self): + """Test that conversion, channel_conversion, and offset are all applied.""" + # Result should be: data * conversion * channel_conversion + offset + # = 1.0 * 2.0 * 3.0 + 1.0 = 7.0 + series = create_mock_electrical_series( + 10, 2, rate=1000.0, conversion=2.0, channel_conversion=[3.0, 4.0], offset=1.0 + ) + series.data = np.ones((10, 2)) + session_start = datetime(2023, 1, 1, 12, 0, 0) + + reader = NWBElectricalSeriesReader(series, session_start) + chunk = reader.get_chunk(0) + + np.testing.assert_array_equal(chunk, np.ones(10) * 7.0) diff --git a/tests/test_timeseries_channel.py b/tests/test_timeseries_channel.py new file mode 100644 index 0000000..5a816b8 --- /dev/null +++ b/tests/test_timeseries_channel.py @@ -0,0 +1,305 @@ +import pytest +from timeseries_channel import TimeSeriesChannel + + +class TestTimeSeriesChannelInit: + """Tests for TimeSeriesChannel initialization.""" + + def test_basic_initialization(self): + """Test basic channel creation with required parameters.""" + channel = TimeSeriesChannel(index=0, name="Test Channel", rate=30000.0, start=1000000, end=2000000) + + assert channel.index == 0 + assert channel.name == "Test Channel" + assert channel.rate == 30000.0 + assert channel.start == 1000000 + assert channel.end == 2000000 + assert channel.type == "CONTINUOUS" + assert channel.unit == "uV" + assert channel.group == "default" + assert channel.last_annotation == 0 + assert channel.properties == [] + assert channel.id is None + + def test_initialization_with_all_parameters(self): + """Test channel creation with all parameters specified.""" + channel = TimeSeriesChannel( + index=5, + name=" Channel 5 ", + rate=10000.0, + start=500000, + end=1500000, + type="UNIT", + unit=" mV ", + group=" electrode_group ", + last_annotation=100, + properties=[{"key": "value"}], + id="N:channel:123", + ) + + assert channel.index == 5 + assert channel.name == "Channel 5" # should be stripped + assert channel.rate == 10000.0 + assert channel.start == 500000 + assert channel.end == 1500000 + assert channel.type == "UNIT" # should be uppercased + assert channel.unit == "mV" # should be stripped + assert channel.group == "electrode_group" # should be stripped + assert channel.last_annotation == 100 + assert channel.properties == [{"key": "value"}] + assert channel.id == "N:channel:123" + + def test_type_case_insensitive(self): + """Test that type is converted to uppercase.""" + channel = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000, type="continuous") + assert channel.type == "CONTINUOUS" + + channel2 = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000, type="Unit") + assert channel2.type == "UNIT" + + def test_invalid_type_raises_assertion(self): + """Test that invalid type raises AssertionError.""" + with pytest.raises(AssertionError, match="Type must be CONTINUOUS or UNIT"): + TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000, type="INVALID") + + def test_start_end_converted_to_int(self): + """Test that start and end are converted to integers.""" + channel = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=1000000.5, end=2000000.9) + assert channel.start == 1000000 + assert channel.end == 2000000 + assert isinstance(channel.start, int) + assert isinstance(channel.end, int) + + +class TestTimeSeriesChannelAsDict: + """Tests for TimeSeriesChannel.as_dict() method.""" + + def test_as_dict_without_id(self): + """Test as_dict when id is None.""" + channel = TimeSeriesChannel(index=0, name="Test Channel", rate=30000.0, start=1000000, end=2000000) + + result = channel.as_dict() + + assert result == { + "name": "Test Channel", + "start": 1000000, + "end": 2000000, + "unit": "uV", + "rate": 30000.0, + "type": "CONTINUOUS", + "group": "default", + "lastAnnotation": 0, + "properties": [], + } + assert "id" not in result + + def test_as_dict_with_id(self): + """Test as_dict when id is set.""" + channel = TimeSeriesChannel( + index=0, name="Test Channel", rate=30000.0, start=1000000, end=2000000, id="N:channel:abc-123" + ) + + result = channel.as_dict() + + assert "id" in result + assert result["id"] == "N:channel:abc-123" + + def test_as_dict_with_custom_properties(self): + """Test as_dict with custom properties.""" + channel = TimeSeriesChannel( + index=0, name="Test", rate=1000.0, start=0, end=1000, properties=[{"key1": "value1"}, {"key2": "value2"}] + ) + + result = channel.as_dict() + assert result["properties"] == [{"key1": "value1"}, {"key2": "value2"}] + + +class TestTimeSeriesChannelFromDict: + """Tests for TimeSeriesChannel.from_dict() static method.""" + + def test_from_dict_with_type_key(self, sample_channel_dict): + """Test from_dict with 'type' key.""" + channel = TimeSeriesChannel.from_dict(sample_channel_dict) + + assert channel.name == "Channel 1" + assert channel.start == 1000000 + assert channel.end == 2000000 + assert channel.unit == "uV" + assert channel.rate == 30000.0 + assert channel.type == "CONTINUOUS" + assert channel.group == "default" + assert channel.last_annotation == 0 + assert channel.id == "N:channel:test-id-123" + assert channel.index == -1 # Default when from_dict + + def test_from_dict_with_channel_type_key(self, sample_channel_dict_with_channel_type): + """Test from_dict with 'channelType' key (API format).""" + channel = TimeSeriesChannel.from_dict(sample_channel_dict_with_channel_type) + + assert channel.type == "CONTINUOUS" + + def test_from_dict_with_properties_override(self): + """Test from_dict with properties parameter override.""" + channel_dict = { + "name": "Channel 1", + "start": 1000000, + "end": 2000000, + "unit": "uV", + "rate": 30000.0, + "type": "CONTINUOUS", + "group": "default", + } + custom_props = [{"custom": "property"}] + + channel = TimeSeriesChannel.from_dict(channel_dict, properties=custom_props) + + assert channel.properties == custom_props + + def test_from_dict_without_optional_fields(self): + """Test from_dict with minimal required fields.""" + minimal_dict = { + "name": "Minimal Channel", + "start": 0, + "end": 1000, + "unit": "uV", + "rate": 1000.0, + "type": "CONTINUOUS", + "group": "default", + } + + channel = TimeSeriesChannel.from_dict(minimal_dict) + + assert channel.name == "Minimal Channel" + assert channel.last_annotation == 0 + assert channel.id is None + + def test_from_dict_start_end_converted_to_int(self): + """Test that from_dict converts start/end to int.""" + data = { + "name": "Test", + "start": "1000000", + "end": "2000000", + "unit": "uV", + "rate": 1000.0, + "type": "CONTINUOUS", + "group": "default", + } + + channel = TimeSeriesChannel.from_dict(data) + + assert channel.start == 1000000 + assert channel.end == 2000000 + + +class TestTimeSeriesChannelEquality: + """Tests for TimeSeriesChannel custom equality comparison.""" + + def test_equal_channels(self): + """Test that channels with same name, type, and similar rate are equal.""" + channel1 = TimeSeriesChannel(index=0, name="Test Channel", rate=30000.0, start=1000000, end=2000000) + channel2 = TimeSeriesChannel( + index=1, # Different index + name="Test Channel", + rate=30000.0, + start=3000000, # Different start + end=4000000, # Different end + ) + + assert channel1 == channel2 + + def test_equal_channels_case_insensitive_name(self): + """Test that name comparison is case-insensitive.""" + channel1 = TimeSeriesChannel(index=0, name="Test Channel", rate=30000.0, start=0, end=1000) + channel2 = TimeSeriesChannel(index=0, name="TEST CHANNEL", rate=30000.0, start=0, end=1000) + + assert channel1 == channel2 + + def test_equal_channels_case_insensitive_type(self): + """Test that type comparison is case-insensitive.""" + channel1 = TimeSeriesChannel(index=0, name="Test", rate=30000.0, start=0, end=1000, type="CONTINUOUS") + channel2 = TimeSeriesChannel(index=0, name="Test", rate=30000.0, start=0, end=1000, type="continuous") + + assert channel1 == channel2 + + def test_equal_channels_rate_within_2_percent(self): + """Test that channels with rate within 2% are equal.""" + channel1 = TimeSeriesChannel(index=0, name="Test", rate=30000.0, start=0, end=1000) + # 1.5% difference + channel2 = TimeSeriesChannel(index=0, name="Test", rate=30450.0, start=0, end=1000) + + assert channel1 == channel2 + + def test_not_equal_different_name(self): + """Test that channels with different names are not equal.""" + channel1 = TimeSeriesChannel(index=0, name="Channel A", rate=30000.0, start=0, end=1000) + channel2 = TimeSeriesChannel(index=0, name="Channel B", rate=30000.0, start=0, end=1000) + + assert channel1 != channel2 + + def test_not_equal_different_type(self): + """Test that channels with different types are not equal.""" + channel1 = TimeSeriesChannel(index=0, name="Test", rate=30000.0, start=0, end=1000, type="CONTINUOUS") + channel2 = TimeSeriesChannel(index=0, name="Test", rate=30000.0, start=0, end=1000, type="UNIT") + + assert channel1 != channel2 + + def test_not_equal_rate_beyond_2_percent(self): + """Test that channels with rate difference > 2% are not equal.""" + channel1 = TimeSeriesChannel(index=0, name="Test", rate=30000.0, start=0, end=1000) + # 3% difference + channel2 = TimeSeriesChannel(index=0, name="Test", rate=30900.0, start=0, end=1000) + + assert channel1 != channel2 + + def test_equality_boundary_exactly_2_percent(self): + """Test equality at exactly 2% rate difference boundary.""" + channel1 = TimeSeriesChannel(index=0, name="Test", rate=30000.0, start=0, end=1000) + # Just over 2% difference - should NOT be equal (< 0.02 check) + # The check is: abs(1-(self.rate/other.rate)) < 0.02 + # At 30600: abs(1-(30000/30600)) = abs(1-0.9804) = 0.0196 < 0.02 - EQUAL + # At 30700: abs(1-(30000/30700)) = abs(1-0.9772) = 0.0228 > 0.02 - NOT EQUAL + channel2 = TimeSeriesChannel( + index=0, + name="Test", + rate=30700.0, # Just over 2% + start=0, + end=1000, + ) + + assert channel1 != channel2 + + +class TestTimeSeriesChannelRoundTrip: + """Tests for round-trip serialization/deserialization.""" + + def test_as_dict_from_dict_round_trip(self): + """Test that as_dict() -> from_dict() preserves data.""" + original = TimeSeriesChannel( + index=5, + name="Round Trip Channel", + rate=20000.0, + start=500000, + end=1500000, + type="UNIT", + unit="mV", + group="test_group", + last_annotation=50, + properties=[{"key": "value"}], + id="N:channel:round-trip", + ) + + serialized = original.as_dict() + restored = TimeSeriesChannel.from_dict(serialized) + + assert restored.name == original.name + assert restored.rate == original.rate + assert restored.start == original.start + assert restored.end == original.end + assert restored.type == original.type + assert restored.unit == original.unit + assert restored.group == original.group + assert restored.last_annotation == original.last_annotation + assert restored.properties == original.properties + assert restored.id == original.id + # Index is not serialized, restored should be -1 + assert restored.index == -1 diff --git a/tests/test_timeseries_client.py b/tests/test_timeseries_client.py new file mode 100644 index 0000000..6171431 --- /dev/null +++ b/tests/test_timeseries_client.py @@ -0,0 +1,276 @@ +import json + +import pytest +import responses +from clients.timeseries_client import TimeSeriesClient +from timeseries_channel import TimeSeriesChannel + + +class TestTimeSeriesClientInit: + """Tests for TimeSeriesClient initialization.""" + + def test_initialization(self, mock_session_manager): + """Test basic initialization.""" + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + + assert client.api_host == "https://api.test.com" + assert client.session_manager == mock_session_manager + + +class TestTimeSeriesClientCreateChannel: + """Tests for TimeSeriesClient.create_channel method.""" + + @responses.activate + def test_create_channel_success(self, mock_session_manager): + """Test successful channel creation.""" + responses.add( + responses.POST, + "https://api.test.com/timeseries/pkg-123/channels", + json={ + "content": { + "id": "N:channel:new-id-456", + "name": "Test Channel", + "start": 1000000, + "end": 2000000, + "unit": "uV", + "rate": 30000.0, + "channelType": "CONTINUOUS", + "group": "default", + "lastAnnotation": 0, + }, + "properties": [{"key": "value"}], + }, + status=200, + ) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + channel = TimeSeriesChannel(index=5, name="Test Channel", rate=30000.0, start=1000000, end=2000000) + + result = client.create_channel("pkg-123", channel) + + assert result.id == "N:channel:new-id-456" + assert result.name == "Test Channel" + assert result.index == 5 # Index should be preserved from input + + @responses.activate + def test_create_channel_sends_correct_body(self, mock_session_manager): + """Test that create_channel sends correct request body.""" + responses.add( + responses.POST, + "https://api.test.com/timeseries/pkg-123/channels", + json={ + "content": { + "id": "N:channel:id", + "name": "Ch1", + "start": 0, + "end": 1000, + "unit": "mV", + "rate": 1000.0, + "channelType": "UNIT", + "group": "test_group", + }, + "properties": [], + }, + status=200, + ) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + channel = TimeSeriesChannel( + index=0, name="Ch1", rate=1000.0, start=0, end=1000, type="UNIT", unit="mV", group="test_group" + ) + + client.create_channel("pkg-123", channel) + + body = json.loads(responses.calls[0].request.body) + assert body["name"] == "Ch1" + assert body["rate"] == 1000.0 + assert body["channelType"] == "UNIT" # 'type' should be renamed to 'channelType' + assert "type" not in body # Original 'type' key should be removed + assert body["unit"] == "mV" + assert body["group"] == "test_group" + + @responses.activate + def test_create_channel_includes_auth_header(self, mock_session_manager): + """Test that authorization header is included.""" + responses.add( + responses.POST, + "https://api.test.com/timeseries/pkg-123/channels", + json={ + "content": { + "id": "N:channel:id", + "name": "Ch1", + "start": 0, + "end": 1000, + "unit": "uV", + "rate": 1000.0, + "channelType": "CONTINUOUS", + "group": "default", + }, + "properties": [], + }, + status=200, + ) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + channel = TimeSeriesChannel(index=0, name="Ch1", rate=1000.0, start=0, end=1000) + + client.create_channel("pkg-123", channel) + + assert responses.calls[0].request.headers["Authorization"] == "Bearer mock-token-12345" + + @responses.activate + def test_create_channel_raises_on_http_error(self, mock_session_manager): + """Test that HTTP errors are raised.""" + responses.add( + responses.POST, + "https://api.test.com/timeseries/pkg-123/channels", + json={"error": "Bad request"}, + status=400, + ) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + channel = TimeSeriesChannel(index=0, name="Ch1", rate=1000.0, start=0, end=1000) + + with pytest.raises(Exception): + client.create_channel("pkg-123", channel) + + +class TestTimeSeriesClientGetPackageChannels: + """Tests for TimeSeriesClient.get_package_channels method.""" + + @responses.activate + def test_get_package_channels_success(self, mock_session_manager): + """Test successful channel retrieval.""" + responses.add( + responses.GET, + "https://api.test.com/timeseries/pkg-123/channels", + json=[ + { + "content": { + "id": "N:channel:ch1", + "name": "Channel 1", + "start": 0, + "end": 1000, + "unit": "uV", + "rate": 30000.0, + "channelType": "CONTINUOUS", + "group": "group_a", + }, + "properties": [{"key": "value1"}], + }, + { + "content": { + "id": "N:channel:ch2", + "name": "Channel 2", + "start": 0, + "end": 1000, + "unit": "mV", + "rate": 1000.0, + "channelType": "UNIT", + "group": "group_b", + }, + "properties": [{"key": "value2"}], + }, + ], + status=200, + ) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + channels = client.get_package_channels("pkg-123") + + assert len(channels) == 2 + assert channels[0].name == "Channel 1" + assert channels[0].id == "N:channel:ch1" + assert channels[0].rate == 30000.0 + assert channels[1].name == "Channel 2" + assert channels[1].type == "UNIT" + + @responses.activate + def test_get_package_channels_empty_list(self, mock_session_manager): + """Test retrieval of empty channel list.""" + responses.add(responses.GET, "https://api.test.com/timeseries/pkg-123/channels", json=[], status=200) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + channels = client.get_package_channels("pkg-123") + + assert channels == [] + + @responses.activate + def test_get_package_channels_includes_auth_header(self, mock_session_manager): + """Test that authorization header is included.""" + responses.add(responses.GET, "https://api.test.com/timeseries/pkg-123/channels", json=[], status=200) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + client.get_package_channels("pkg-123") + + assert responses.calls[0].request.headers["Authorization"] == "Bearer mock-token-12345" + + @responses.activate + def test_get_package_channels_raises_on_http_error(self, mock_session_manager): + """Test that HTTP errors are raised.""" + responses.add( + responses.GET, "https://api.test.com/timeseries/pkg-123/channels", json={"error": "Not found"}, status=404 + ) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + + with pytest.raises(Exception): + client.get_package_channels("pkg-123") + + +class TestTimeSeriesClientRetryBehavior: + """Tests for retry behavior with session refresh.""" + + @responses.activate + def test_create_channel_retries_on_401(self, mock_session_manager): + """Test that create_channel retries after 401.""" + # First call returns 401 + responses.add( + responses.POST, + "https://api.test.com/timeseries/pkg-123/channels", + json={"error": "Unauthorized"}, + status=401, + ) + # Second call succeeds + responses.add( + responses.POST, + "https://api.test.com/timeseries/pkg-123/channels", + json={ + "content": { + "id": "N:channel:id", + "name": "Ch1", + "start": 0, + "end": 1000, + "unit": "uV", + "rate": 1000.0, + "channelType": "CONTINUOUS", + "group": "default", + }, + "properties": [], + }, + status=200, + ) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + channel = TimeSeriesChannel(index=0, name="Ch1", rate=1000.0, start=0, end=1000) + + result = client.create_channel("pkg-123", channel) + + assert result.id == "N:channel:id" + mock_session_manager.refresh_session.assert_called_once() + + @responses.activate + def test_get_package_channels_retries_on_403(self, mock_session_manager): + """Test that get_package_channels retries after 403.""" + # First call returns 403 + responses.add( + responses.GET, "https://api.test.com/timeseries/pkg-123/channels", json={"error": "Forbidden"}, status=403 + ) + # Second call succeeds + responses.add(responses.GET, "https://api.test.com/timeseries/pkg-123/channels", json=[], status=200) + + client = TimeSeriesClient("https://api.test.com", mock_session_manager) + channels = client.get_package_channels("pkg-123") + + assert channels == [] + mock_session_manager.refresh_session.assert_called_once() diff --git a/tests/test_utils.py b/tests/test_utils.py new file mode 100644 index 0000000..97cc374 --- /dev/null +++ b/tests/test_utils.py @@ -0,0 +1,153 @@ +import sys + +import numpy as np +from utils import infer_sampling_rate, to_big_endian + + +class TestInferSamplingRate: + """Tests for infer_sampling_rate function.""" + + def test_1000hz_sampling_rate(self): + """Test inference from 1000 Hz sampling rate timestamps.""" + # 1000 Hz = 0.001 second period + timestamps = np.linspace(0, 0.1, 100, endpoint=False) + rate = infer_sampling_rate(timestamps) + assert abs(rate - 1000.0) < 1.0 # Allow small floating point error + + def test_30000hz_sampling_rate(self): + """Test inference from 30000 Hz sampling rate timestamps.""" + # 30000 Hz = 0.0000333... second period + timestamps = np.linspace(0, 0.001, 30, endpoint=False) + rate = infer_sampling_rate(timestamps) + assert abs(rate - 30000.0) < 1.0 + + def test_uses_first_10_timestamps(self): + """Test that only first 10 timestamps are used for inference.""" + # First 10 timestamps at 1000 Hz + first_10 = np.linspace(0, 0.01, 10, endpoint=False) + # Rest at different rate (this should be ignored) + rest = np.linspace(0.01, 0.1, 90, endpoint=False) + timestamps = np.concatenate([first_10, rest]) + + rate = infer_sampling_rate(timestamps) + assert abs(rate - 1000.0) < 1.0 + + def test_fewer_than_10_timestamps(self): + """Test inference with fewer than 10 timestamps.""" + timestamps = np.linspace(0, 0.005, 5, endpoint=False) + rate = infer_sampling_rate(timestamps) + assert abs(rate - 1000.0) < 1.0 + + def test_minimum_2_timestamps(self): + """Test inference with exactly 2 timestamps.""" + timestamps = np.array([0.0, 0.001]) + rate = infer_sampling_rate(timestamps) + assert abs(rate - 1000.0) < 0.1 + + def test_irregular_timestamps_uses_median(self): + """Test that median is used for slightly irregular timestamps.""" + # Create timestamps with slight irregularity + # 9 intervals, most at 0.001 (1000 Hz) + timestamps = np.array( + [ + 0.000, + 0.001, + 0.002, + 0.003, + 0.004, + 0.0051, # slight irregularity + 0.006, + 0.007, + 0.008, + 0.009, + ] + ) + rate = infer_sampling_rate(timestamps) + # Median should still be ~0.001 + assert abs(rate - 1000.0) < 10.0 + + +class TestToBigEndian: + """Tests for to_big_endian function.""" + + def test_little_endian_conversion(self): + """Test conversion from little endian to big endian.""" + # Create explicitly little-endian array + data = np.array([1.0, 2.0, 3.0], dtype="", "|") # '|' for byte-order neutral + # Values should be preserved + np.testing.assert_array_equal(result, [1.0, 2.0, 3.0]) + + def test_big_endian_no_change(self): + """Test that big endian arrays are not modified.""" + data = np.array([1.0, 2.0, 3.0], dtype=">f8") # big-endian float64 + result = to_big_endian(data) + + assert result.dtype.byteorder == ">" + np.testing.assert_array_equal(result, [1.0, 2.0, 3.0]) + + def test_native_endian_on_little_endian_system(self): + """Test native endian conversion on little-endian system.""" + data = np.array([1.0, 2.0, 3.0], dtype=np.float64) # native endian + + result = to_big_endian(data) + + # On little-endian system, should be converted + # On big-endian system, should remain unchanged + if sys.byteorder == "little": + assert result.dtype.byteorder in (">", "|") + else: + assert result.dtype.byteorder in (">", "=", "|") + + def test_preserves_array_values(self): + """Test that array values are preserved after conversion.""" + original = np.array([1.5, -2.5, 0.0, 1e10, 1e-10], dtype=np.float64) + result = to_big_endian(original.copy()) + + np.testing.assert_array_almost_equal(result, original) + + def test_float32_array(self): + """Test conversion of float32 array.""" + data = np.array([1.0, 2.0, 3.0], dtype="" diff --git a/tests/test_workflow_client.py b/tests/test_workflow_client.py new file mode 100644 index 0000000..e1518c7 --- /dev/null +++ b/tests/test_workflow_client.py @@ -0,0 +1,163 @@ +import json + +import pytest +import responses +from clients.workflow_client import WorkflowClient, WorkflowInstance + + +class TestWorkflowInstance: + """Tests for WorkflowInstance class.""" + + def test_initialization(self): + """Test WorkflowInstance initialization.""" + instance = WorkflowInstance(id="workflow-123", dataset_id="dataset-456", package_ids=["pkg-1", "pkg-2"]) + + assert instance.id == "workflow-123" + assert instance.dataset_id == "dataset-456" + assert instance.package_ids == ["pkg-1", "pkg-2"] + + def test_initialization_with_empty_package_ids(self): + """Test WorkflowInstance with empty package list.""" + instance = WorkflowInstance(id="workflow-123", dataset_id="dataset-456", package_ids=[]) + + assert instance.package_ids == [] + + def test_initialization_with_single_package(self): + """Test WorkflowInstance with single package.""" + instance = WorkflowInstance(id="workflow-123", dataset_id="dataset-456", package_ids=["single-pkg"]) + + assert len(instance.package_ids) == 1 + assert instance.package_ids[0] == "single-pkg" + + +class TestWorkflowClientInit: + """Tests for WorkflowClient initialization.""" + + def test_initialization(self, mock_session_manager): + """Test basic initialization.""" + client = WorkflowClient("https://api.test.com", mock_session_manager) + + assert client.api_host == "https://api.test.com" + assert client.session_manager == mock_session_manager + + +class TestWorkflowClientGetWorkflowInstance: + """Tests for WorkflowClient.get_workflow_instance method.""" + + @responses.activate + def test_get_workflow_instance_success(self, mock_session_manager): + """Test successful workflow instance retrieval.""" + responses.add( + responses.GET, + "https://api.test.com/workflows/instances/wf-instance-123", + json={"uuid": "wf-instance-123", "datasetId": "dataset-456", "packageIds": ["pkg-1", "pkg-2", "pkg-3"]}, + status=200, + ) + + client = WorkflowClient("https://api.test.com", mock_session_manager) + result = client.get_workflow_instance("wf-instance-123") + + assert isinstance(result, WorkflowInstance) + assert result.id == "wf-instance-123" + assert result.dataset_id == "dataset-456" + assert result.package_ids == ["pkg-1", "pkg-2", "pkg-3"] + + @responses.activate + def test_get_workflow_instance_includes_auth_header(self, mock_session_manager): + """Test that authorization header is included.""" + responses.add( + responses.GET, + "https://api.test.com/workflows/instances/wf-123", + json={"uuid": "wf-123", "datasetId": "ds-1", "packageIds": []}, + status=200, + ) + + client = WorkflowClient("https://api.test.com", mock_session_manager) + client.get_workflow_instance("wf-123") + + assert responses.calls[0].request.headers["Authorization"] == "Bearer mock-token-12345" + assert responses.calls[0].request.headers["Accept"] == "application/json" + + @responses.activate + def test_get_workflow_instance_raises_on_http_error(self, mock_session_manager): + """Test that HTTP errors are raised.""" + responses.add( + responses.GET, "https://api.test.com/workflows/instances/wf-123", json={"error": "Not found"}, status=404 + ) + + client = WorkflowClient("https://api.test.com", mock_session_manager) + + with pytest.raises(Exception): + client.get_workflow_instance("wf-123") + + @responses.activate + def test_get_workflow_instance_raises_on_invalid_json(self, mock_session_manager): + """Test that invalid JSON raises error.""" + responses.add(responses.GET, "https://api.test.com/workflows/instances/wf-123", body="not json", status=200) + + client = WorkflowClient("https://api.test.com", mock_session_manager) + + with pytest.raises(json.JSONDecodeError): + client.get_workflow_instance("wf-123") + + @responses.activate + def test_get_workflow_instance_with_single_package(self, mock_session_manager): + """Test workflow instance with single package ID.""" + responses.add( + responses.GET, + "https://api.test.com/workflows/instances/wf-123", + json={"uuid": "wf-123", "datasetId": "ds-1", "packageIds": ["single-pkg"]}, + status=200, + ) + + client = WorkflowClient("https://api.test.com", mock_session_manager) + result = client.get_workflow_instance("wf-123") + + assert len(result.package_ids) == 1 + assert result.package_ids[0] == "single-pkg" + + +class TestWorkflowClientRetryBehavior: + """Tests for retry behavior with session refresh.""" + + @responses.activate + def test_get_workflow_instance_retries_on_401(self, mock_session_manager): + """Test that get_workflow_instance retries after 401.""" + # First call returns 401 + responses.add( + responses.GET, "https://api.test.com/workflows/instances/wf-123", json={"error": "Unauthorized"}, status=401 + ) + # Second call succeeds + responses.add( + responses.GET, + "https://api.test.com/workflows/instances/wf-123", + json={"uuid": "wf-123", "datasetId": "ds-1", "packageIds": []}, + status=200, + ) + + client = WorkflowClient("https://api.test.com", mock_session_manager) + result = client.get_workflow_instance("wf-123") + + assert result.id == "wf-123" + mock_session_manager.refresh_session.assert_called_once() + + @responses.activate + def test_get_workflow_instance_retries_on_403(self, mock_session_manager): + """Test that get_workflow_instance retries after 403.""" + # First call returns 403 + responses.add( + responses.GET, "https://api.test.com/workflows/instances/wf-123", json={"error": "Forbidden"}, status=403 + ) + # Second call succeeds + responses.add( + responses.GET, + "https://api.test.com/workflows/instances/wf-123", + json={"uuid": "wf-123", "datasetId": "ds-1", "packageIds": []}, + status=200, + ) + + client = WorkflowClient("https://api.test.com", mock_session_manager) + result = client.get_workflow_instance("wf-123") + + assert result.id == "wf-123" + mock_session_manager.refresh_session.assert_called_once() diff --git a/tests/test_writer.py b/tests/test_writer.py new file mode 100644 index 0000000..4ffabdb --- /dev/null +++ b/tests/test_writer.py @@ -0,0 +1,341 @@ +import gzip +import json +import os +from unittest.mock import Mock, patch + +import numpy as np +from constants import TIME_SERIES_BINARY_FILE_EXTENSION, TIME_SERIES_METADATA_FILE_EXTENSION +from timeseries_channel import TimeSeriesChannel +from writer import TimeSeriesChunkWriter + + +class TestTimeSeriesChunkWriterInit: + """Tests for TimeSeriesChunkWriter initialization.""" + + def test_initialization(self, temp_output_dir, session_start_time): + """Test basic initialization.""" + writer = TimeSeriesChunkWriter( + session_start_time=session_start_time, output_dir=temp_output_dir, chunk_size=1000 + ) + + assert writer.session_start_time == session_start_time + assert writer.output_dir == temp_output_dir + assert writer.chunk_size == 1000 + + +class TestWriteChunk: + """Tests for write_chunk method.""" + + def test_write_chunk_creates_file(self, temp_output_dir, session_start_time): + """Test that write_chunk creates a binary file.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + chunk = np.array([1.0, 2.0, 3.0, 4.0, 5.0], dtype=np.float64) + channel = TimeSeriesChannel(index=0, name="Test Channel", rate=1000.0, start=1000000, end=2000000) + + start_time = 1.0 + end_time = 1.005 + + writer.write_chunk(chunk, start_time, end_time, channel) + + # Check file was created + expected_filename = ( + f"channel-00000_{int(start_time * 1e6)}_{int(end_time * 1e6)}{TIME_SERIES_BINARY_FILE_EXTENSION}" + ) + file_path = os.path.join(temp_output_dir, expected_filename) + assert os.path.exists(file_path) + + def test_write_chunk_gzip_compressed(self, temp_output_dir, session_start_time): + """Test that output file is gzip compressed.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + chunk = np.array([1.0, 2.0, 3.0], dtype=np.float64) + channel = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000) + + writer.write_chunk(chunk, 1.0, 1.003, channel) + + # Find the file (timestamps may vary slightly) + files = [f for f in os.listdir(temp_output_dir) if f.endswith(".bin.gz")] + assert len(files) == 1 + file_path = os.path.join(temp_output_dir, files[0]) + + # Should be readable as gzip + with gzip.open(file_path, "rb") as f: + data = f.read() + assert len(data) > 0 + + def test_write_chunk_big_endian_format(self, temp_output_dir, session_start_time): + """Test that data is written in big-endian format.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + chunk = np.array([1.0, 2.0, 3.0], dtype=np.float64) + channel = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000) + + writer.write_chunk(chunk, 1.0, 1.003, channel) + + # Find the file + files = [f for f in os.listdir(temp_output_dir) if f.endswith(".bin.gz")] + assert len(files) == 1 + file_path = os.path.join(temp_output_dir, files[0]) + + with gzip.open(file_path, "rb") as f: + data = f.read() + + # Read as big-endian float64 + result = np.frombuffer(data, dtype=">f8") + np.testing.assert_array_equal(result, [1.0, 2.0, 3.0]) + + def test_write_chunk_channel_index_formatting(self, temp_output_dir, session_start_time): + """Test that channel index is zero-padded to 5 digits.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + chunk = np.array([1.0], dtype=np.float64) + + # Test various channel indices with unique timestamps to avoid overwriting + for i, index in enumerate([0, 5, 42, 999, 12345]): + channel = TimeSeriesChannel(index=index, name="Test", rate=1000.0, start=0, end=1000) + start_time = 1.0 + i * 0.1 + end_time = start_time + 0.001 + writer.write_chunk(chunk, start_time, end_time, channel) + + # Check that file with correct channel index prefix exists + files = [f for f in os.listdir(temp_output_dir) if f.startswith(f"channel-{index:05d}_")] + assert len(files) >= 1, f"No file found for channel index {index}" + + def test_write_chunk_preserves_data_precision(self, temp_output_dir, session_start_time): + """Test that float64 precision is preserved.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + # Use values that require float64 precision + chunk = np.array([1.123456789012345, -9.87654321098765e10, 1e-15], dtype=np.float64) + channel = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000) + + writer.write_chunk(chunk, 1.0, 1.003, channel) + + # Find the file + files = [f for f in os.listdir(temp_output_dir) if f.endswith(".bin.gz")] + assert len(files) == 1 + file_path = os.path.join(temp_output_dir, files[0]) + + with gzip.open(file_path, "rb") as f: + data = f.read() + + result = np.frombuffer(data, dtype=">f8") + np.testing.assert_array_almost_equal(result, chunk, decimal=14) + + +class TestWriteChannel: + """Tests for write_channel method.""" + + def test_write_channel_creates_metadata_file(self, temp_output_dir, session_start_time): + """Test that write_channel creates a JSON metadata file.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + channel = TimeSeriesChannel( + index=5, name="Test Channel", rate=30000.0, start=1000000, end=2000000, unit="mV", group="electrode_group" + ) + + writer.write_channel(channel) + + expected_filename = f"channel-00005{TIME_SERIES_METADATA_FILE_EXTENSION}" + file_path = os.path.join(temp_output_dir, expected_filename) + assert os.path.exists(file_path) + + def test_write_channel_json_content(self, temp_output_dir, session_start_time): + """Test that metadata file contains correct JSON.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + channel = TimeSeriesChannel( + index=0, + name="Test Channel", + rate=30000.0, + start=1000000, + end=2000000, + unit="mV", + type="CONTINUOUS", + group="test_group", + last_annotation=100, + properties=[{"key": "value"}], + ) + + writer.write_channel(channel) + + file_path = os.path.join(temp_output_dir, "channel-00000.metadata.json") + + with open(file_path, "r") as f: + data = json.load(f) + + assert data["name"] == "Test Channel" + assert data["rate"] == 30000.0 + assert data["start"] == 1000000 + assert data["end"] == 2000000 + assert data["unit"] == "mV" + assert data["type"] == "CONTINUOUS" + assert data["group"] == "test_group" + assert data["lastAnnotation"] == 100 + assert data["properties"] == [{"key": "value"}] + + +class TestWriteElectricalSeries: + """Tests for write_electrical_series method.""" + + def test_write_electrical_series_single_chunk(self, temp_output_dir, session_start_time): + """Test writing electrical series that fits in single chunk.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, chunk_size=1000) + + # Create mock electrical series with 500 samples (less than chunk_size) + mock_reader = Mock() + mock_reader.channels = [TimeSeriesChannel(index=0, name="Ch0", rate=1000.0, start=0, end=1000)] + mock_reader.timestamps = np.linspace(0, 0.5, 500, endpoint=False) + mock_reader.contiguous_chunks.return_value = [(0, 500)] + mock_reader.get_chunk.return_value = np.random.randn(500).astype(np.float64) + + with patch("writer.NWBElectricalSeriesReader", return_value=mock_reader): + mock_series = Mock() + writer.write_electrical_series(mock_series) + + # Should have created 1 binary file and 1 metadata file + files = os.listdir(temp_output_dir) + bin_files = [f for f in files if f.endswith(".bin.gz")] + json_files = [f for f in files if f.endswith(".metadata.json")] + + assert len(bin_files) == 1 + assert len(json_files) == 1 + + def test_write_electrical_series_multiple_chunks(self, temp_output_dir, session_start_time): + """Test writing electrical series that requires multiple chunks.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, chunk_size=100) + + # Create mock with 250 samples, 2 channels + mock_reader = Mock() + mock_reader.channels = [ + TimeSeriesChannel(index=0, name="Ch0", rate=1000.0, start=0, end=1000), + TimeSeriesChannel(index=1, name="Ch1", rate=1000.0, start=0, end=1000), + ] + mock_reader.timestamps = np.linspace(0, 0.25, 250, endpoint=False) + mock_reader.contiguous_chunks.return_value = [(0, 250)] + mock_reader.get_chunk.return_value = np.random.randn(100).astype(np.float64) + + with patch("writer.NWBElectricalSeriesReader", return_value=mock_reader): + mock_series = Mock() + writer.write_electrical_series(mock_series) + + files = os.listdir(temp_output_dir) + bin_files = [f for f in files if f.endswith(".bin.gz")] + json_files = [f for f in files if f.endswith(".metadata.json")] + + # 250 samples / 100 chunk_size = 3 chunks per channel, 2 channels = 6 binary files + assert len(bin_files) == 6 + # 2 metadata files (one per channel) + assert len(json_files) == 2 + + def test_write_electrical_series_with_gap(self, temp_output_dir, session_start_time): + """Test writing electrical series with data gap.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, chunk_size=100) + + mock_reader = Mock() + mock_reader.channels = [TimeSeriesChannel(index=0, name="Ch0", rate=1000.0, start=0, end=1000)] + # Two contiguous segments + timestamps_seg1 = np.linspace(0, 0.1, 100, endpoint=False) + timestamps_seg2 = np.linspace(0.2, 0.3, 100, endpoint=False) + mock_reader.timestamps = np.concatenate([timestamps_seg1, timestamps_seg2]) + mock_reader.contiguous_chunks.return_value = [(0, 100), (100, 200)] + mock_reader.get_chunk.return_value = np.random.randn(100).astype(np.float64) + + with patch("writer.NWBElectricalSeriesReader", return_value=mock_reader): + mock_series = Mock() + writer.write_electrical_series(mock_series) + + files = os.listdir(temp_output_dir) + bin_files = [f for f in files if f.endswith(".bin.gz")] + + # 2 contiguous segments, 1 chunk each = 2 binary files + assert len(bin_files) == 2 + + def test_write_electrical_series_chunk_timestamps(self, temp_output_dir, session_start_time): + """Test that chunk filenames have correct timestamp values.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, chunk_size=50) + + mock_reader = Mock() + mock_reader.channels = [TimeSeriesChannel(index=0, name="Ch0", rate=1000.0, start=0, end=1000)] + # 100 samples at 1000 Hz = 0.1 seconds + mock_reader.timestamps = np.linspace(1.0, 1.1, 100, endpoint=False) + mock_reader.contiguous_chunks.return_value = [(0, 100)] + mock_reader.get_chunk.return_value = np.random.randn(50).astype(np.float64) + + with patch("writer.NWBElectricalSeriesReader", return_value=mock_reader): + mock_series = Mock() + writer.write_electrical_series(mock_series) + + files = os.listdir(temp_output_dir) + bin_files = sorted([f for f in files if f.endswith(".bin.gz")]) + + # First chunk: timestamps[0] to timestamps[49] + # Second chunk: timestamps[50] to timestamps[99] + assert len(bin_files) == 2 + + # Check first chunk filename contains correct timestamps + assert "1000000_1049000" in bin_files[0] # 1.0 to 1.049 seconds in microseconds + assert "1050000_1099000" in bin_files[1] # 1.05 to 1.099 seconds + + +class TestWriteChunkEdgeCases: + """Edge case tests for chunk writing.""" + + def test_write_empty_chunk(self, temp_output_dir, session_start_time): + """Test writing an empty chunk.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + chunk = np.array([], dtype=np.float64) + channel = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000) + + writer.write_chunk(chunk, 1.0, 1.0, channel) + + file_path = os.path.join(temp_output_dir, "channel-00000_1000000_1000000.bin.gz") + + with gzip.open(file_path, "rb") as f: + data = f.read() + + assert len(data) == 0 + + def test_write_large_chunk(self, temp_output_dir, session_start_time): + """Test writing a large chunk.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + # 1 million samples + chunk = np.random.randn(1000000).astype(np.float64) + channel = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000) + + writer.write_chunk(chunk, 0.0, 1000.0, channel) + + file_path = os.path.join(temp_output_dir, "channel-00000_0_1000000000.bin.gz") + assert os.path.exists(file_path) + + # Verify data integrity + with gzip.open(file_path, "rb") as f: + data = f.read() + + result = np.frombuffer(data, dtype=">f8") + assert len(result) == 1000000 + + def test_write_chunk_special_float_values(self, temp_output_dir, session_start_time): + """Test writing chunks with special float values.""" + writer = TimeSeriesChunkWriter(session_start_time, temp_output_dir, 1000) + + chunk = np.array([np.inf, -np.inf, np.nan, 0.0, -0.0], dtype=np.float64) + channel = TimeSeriesChannel(index=0, name="Test", rate=1000.0, start=0, end=1000) + + writer.write_chunk(chunk, 1.0, 1.005, channel) + + # Find the file + files = [f for f in os.listdir(temp_output_dir) if f.endswith(".bin.gz")] + assert len(files) == 1 + file_path = os.path.join(temp_output_dir, files[0]) + + with gzip.open(file_path, "rb") as f: + data = f.read() + + result = np.frombuffer(data, dtype=">f8") + assert np.isinf(result[0]) and result[0] > 0 + assert np.isinf(result[1]) and result[1] < 0 + assert np.isnan(result[2])