minder.research-data-snapshots 0.15.0

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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/

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 --dataset patients raw_heart_rate --organization ELM4RQF8R9dsU3CZEgtiTW 7LcACpK4u12HH72D1etd5X

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

If you only intend to use the command line interface then you can use pipx to prevent clashes with other package versions and to avoid installation altogether:

pipx run minder.research-data-snapshots

Library

python -m pip install 'pandas[parquet]'

from datetime import datetime

import pandas as pd

from minder.research_data_snapshots import download_datasets

path = download_datasets(["patients"], ["ELM4RQF8R9dsU3CZEgtiTW"])[0]
df = pd.read_parquet(path)
print(df)

paths = download_datasets(["raw_heart_rate"])
df = pd.concat(
    pd.read_parquet(
        path,
        filters=[
            ("start_date", ">=", datetime.fromisoformat("2023-01-01T00Z")),
            ("start_date", "<", datetime.fromisoformat("2024-01-01T00Z")),
        ],
        columns=["id", "patient_id", "start_date"],
    )
    for path in paths
).sort_values("start_date").reset_index(drop=True)