minder.research-data-snapshots 0.20.0

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minder.research-data-snapshots

Install

python -m pip install minder.research-data-snapshots

This will provide exports in Parquet format, which should be sufficient if you're using Pandas or another dataframe library.

If you require exports in CSV format then use:

python -m pip install 'minder.research-data-snapshots[csv]'

Use

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

Then use one of the following methods to retrieve data snapshots

CLI

python -m minder.research_data_snapshots --dataset patients raw_heart_rate --organization SABP "H&F" --token-path /path/to/access/token

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

Library

python -m pip install 'pandas[parquet]'

export RESEARCH_PORTAL_TOKEN_PATH=/path/to/access/token

import tempfile
from datetime import datetime
from pathlib import Path

import pandas as pd

from minder.research_data_snapshots import download_datasets

path = download_datasets(["patients"], ["SABP"])[0]
df = pd.read_parquet(path)
print(df)

folder = Path(tempfile.gettempdir()) / "research-data-snapshots"
download_datasets(["patients", "raw_heart_rate"], folder=folder)
df = (
    pd.read_parquet(
        folder / "raw_heart_rate",
        filters=[
            ("start_date", ">=", datetime.fromisoformat("2023-01-01T00Z")),
            ("start_date", "<", datetime.fromisoformat("2024-01-01T00Z")),
        ],
        columns=["patient_id", "start_date", "value"],
    )
    .sort_values("start_date")
    .reset_index(drop=True)
)
print(df)