https://github.com/daylily-informatics/xcures_day

python wrapper for the xcures REST api
https://github.com/daylily-informatics/xcures_day

Last synced: about 9 hours ago
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python wrapper for the xcures REST api

• Host: GitHub
• URL: https://github.com/daylily-informatics/xcures_day
• Owner: Daylily-Informatics
• License: mit
• Created: 2024-06-25T01:15:55.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2024-06-25T03:14:25.000Z (5 months ago)
• Last Synced: 2024-06-25T04:29:19.098Z (5 months ago)
• Language: Python
• Size: 5.86 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# xcures_day

python wrapper for the xcures REST api.

## Status == UNSTABLEish

* The auth functionality is working.

* Subject API query is working, but not tested extensively.

* Other API hooks, ie: query, are not implemented in a trusted way quite yet.

* TODO: I'll benefit from a quick discussion w/the Xcures tech team.

# Configuruartion

## Environment

### Conda

* [Install Miniconda](https://docs.anaconda.com/miniconda/miniconda-install/)

* Create a new environment.

```bash

conda create -y -n XCDAY -c conda-forge python=3.10 ipython pytest pip pytz requests ipython && conda activate XCDAY && pip install yaml_config_day

```

* Activate the environment

```bash

conda activate XCDAY

```

## YAML File

* Located in `~/.config/xcures/xcures_$XCURES_ENV.yaml`, where `XCURES_ENV=` might be `prod` or `test`.

* Contents:

  

```bash

export XCURES_ENV=prod

more ~/.config/xcures/xcures_$XCURES_ENV.yaml

```

```yaml

---

base_url: "https://partner.xcures.com"

base_auth_url: "https://xcures-patient-registry-prod.us.auth0.com"

project_id: "PROJECTIDHERE"

client_id: "CLIENTIDHERE"

client_secret: "SECRETKEYHERE"

```

# Usage

_given the env is set and the yaml file is configured_

## Authenticate

```python

from xcures.xcures_api import XCuresAPI as xc_api

xc = xc_api()

print(xc)

# prints something like 

print(x.token)

# token printed

```

## Crude Test

```python

conda activate XCDAY

python xcures/xcures_api.py # just for quick dev, this will be moved to proper pytest.

```