https://github.com/Clinical-Pharmacy-Saarland-University/abdataapi
Plumber API for ABDATA DDI Checks
https://github.com/Clinical-Pharmacy-Saarland-University/abdataapi
Last synced: about 2 months ago
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Plumber API for ABDATA DDI Checks
- Host: GitHub
- URL: https://github.com/Clinical-Pharmacy-Saarland-University/abdataapi
- Owner: Clinical-Pharmacy-Saarland-University
- License: gpl-3.0
- Created: 2023-08-28T17:46:35.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-07-17T21:09:46.000Z (9 months ago)
- Last Synced: 2024-07-18T01:26:29.528Z (9 months ago)
- Language: HTML
- Size: 1000 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ABDATA Database API
[](https://www.repostatus.org/#active/) [](https://github.com/Clinical-Pharmacy-Saarland-University/nmrunner/) [](https://cran.r-project.org/)
## Description
This repository provides a RESTful API for the ABDATA DDI Checks.
The API is based on the plumber package and provides endpoints for the operations specified in [the manual](manual/manual.md).
This repository does **not** provide the ABDA data base.
## Requirements
1. The application should run on Windows and Linux.
2. To the start the application you need a runtime of at least `R Version 4.1`
and packages listed in `src/helper/packages.R`.
3. Is is highly recommended to use the `just` command line tool to run the commands in the `justfile`. The `just` command line tool can be installed via the following command:
```bash
winget install just # windows
apt-get install just # linux
```
## Quick Start
Thse steps will install or update the necessary packages, initialize the application settings file and start the application.
```bash
just rpkg
just init
just start
```
After configuration via `secrets.json` you can also start the application via the following command:
```r
setwd("src")
source("start_api.R")
```
## Settings File
Provide `secrets.json` file in the `src` directory. The file should provide credentials for your data base instances in the following format:
```json
{
"sql": {
"host": "db_host",
"user": "db_user",
"pwd": "db_pwd",
"port": 0000,
"database": "db_name"
},
"userdb": {
"collection": "user_collection",
"db": "db_for_users",
"url": "url_to_mongodb"
},
"log_db": {
"collection": "logs_collection",
"db": "db_for_logs",
"url": "url_to_mongodb"
},
"token": {
"token_salt": "token_salt"
},
"server": {
"host": "host",
"port": 0001
}
}
```
## Management
**TODO**
## Developement
The following just commands are available for development:
```bash
just doc # render the index.html file from the manual.md in manual directory (needs `pandoc`)
just init-hooks # install git pre-commit hooks (needs python3 installed)
just watch # watch the src directory for changes and restart the api (needs `watchexec`)
```
Install `pandoc` and `watchexec` via the following commands in windows:
```bash
winget install pandoc
scoop install [email protected]
```
## API Endpoint Tests
Test are implemented in the `tests` directory (file `api_test.R`).
1. Install test related `r` packages via the following command:
```bash
just test-rpkg
```
2. Initalize login credentatls and host information via:
```bash
just test-init
```
Edit the files `dev_credentials.yaml` and `prod_credentials.yaml` in the `tests` directory to provide the necessary information.
3. Tests for development and production environment can be run via the following commands:
```bash
just test-dev
just test-prod
```