aind-metadata-extractor 0.3.0

Generated from aind-library-template

aind-metadata-extractor

Install

You should only install the dependencies for the specific extractor you plan to run. You can see the list of available extractors in the pyproject.toml file or in the folders in src/aind_metadata/extractor

During installation pass the extractor as an optional dependency:

pip install 'aind-metadata-extractor[<your-extractor>]'

Run

Each extractor uses a JobSettings object to collect necessary information about data and metadata files to create an Extractor which is run by calling .extract(). For example, for smartspim:

from pathlib import Path

from aind_metadata_extractor.smartspim.job_settings import JobSettings
from aind_metadata_extractor.smartspim.extractor import SmartspimExtractor

DATA_DIR = Path("<path-to-your-data>)

job_settings=JobSettings(
    subject_id="786846",
    metadata_service_path="http://aind-metadata-service/slims/smartspim_imaging",
    input_source=DATA_DIR+"SmartSPIM_786846_2025-04-22_16-44-50",
    slims_datetime="2025-0422T18:30:08.915000Z"
)
extractor = SmartspimExtractor(job_settings=job_settings)
response = extractor.extract()