minder.research-data-snapshots 0.3

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minder.research-data-snapshots

Install

pip install minder.research-data-snapshots

Use

First retrieve an access token from https://research.minder.care/

export RESEARCH_PORTAL_TOKEN_PATH=/path/to/access/token

Then use one of the following methods to retrieve data snapshots

CLI

python -m minder.research_data_snapshots --organization ELM4RQF8R9dsU3CZEgtiTW 7LcACpK4u12HH72D1etd5X --dataset patients raw_heart_rate

Run python -m minder.research_data_snapshots --help to see all options

Library

from datetime import datetime

import pandas as pd

from minder.research_data_snapshots import download_dataset, download_datasets

path = download_dataset("ELM4RQF8R9dsU3CZEgtiTW", "patients")
df = pd.read_parquet(path)
print(df)

paths = download_datasets(["ELM4RQF8R9dsU3CZEgtiTW", "7LcACpK4u12HH72D1etd5X"], ["raw_heart_rate"])
df = (
    pd.read_parquet(
        paths,
        filters=[
            ("start_date", ">=", datetime.fromisoformat("2023-01-01T00Z")),
            ("start_date", "<", datetime.fromisoformat("2024-01-01T00Z")),
        ],
    )
    .sort_values("start_date")
    .reset_index(drop=True)
)
print(df)