minder.research_portal_client 0.1.1

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Research Portal Client

Library to interact with Minder Research APIs.

Example

import logging
import asyncio
import datetime
from minder.research_portal_client import Configuration, JobManager
from minder.research_portal_client.models import ExportJobRequest, ExportJobRequestDataset


logging.basicConfig(level="INFO")

Configuration.set_default(
    Configuration(
        access_token="---REDACTED---",
    )
)


async def example1():
    async with JobManager() as job_manager:
        now = datetime.datetime.today()
        since = now - datetime.timedelta(days=7)
        datasets: dict(str, ExportJobRequestDataset) = {
            "patients": ExportJobRequestDataset(),
            "observation_notes": ExportJobRequestDataset(),
        }

        export_job = ExportJobRequest(since, datasets=datasets)
        job_id = await job_manager.submit(export_job)
        job = await job_manager.wait(job_id)
        await job_manager.download(job)


async def example2():
    job_id = "c25249e0-82ff-43d1-9676-f3cead0228b9"
    async with JobManager() as job_manager:
        await job_manager.download(job_id)

async def example3():
    async with JobManager() as job_manager:
        datasets = await job_manager.client.info.list_datasets()
        print(datasets)

        organizations = await job_manager.client.info.list_organizations()
        print(organizations)

        reports = await job_manager.client.reports.list_reports()
        print(reports)


async def main():
    await example1()
    await example2()
    await example3()


loop = asyncio.get_event_loop()
loop.run_until_complete(main())

Development

Useful commands

Run tests

poetry run pytest

Code Coverage

This command consists of 2 parts:

• running tests with coverage collection
• formatting the report: report (text to stdout), xml (GitLab compatible: cobertura), html (visual)

poetry run coverage run -m pytest && poetry run coverage report -m

Linting

poetry run flake8

Formatting

poetry run black .

Type Checking

poetry run mypy .