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Add links to components + cleanup backtics
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clemens-tolboom committed Dec 4, 2023
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You can run from source code as follows:

1. Install Java and Docker
2. Checkout the source using ```git clone https://github.com/molgenis/molgenis-service-armadillo.git```
3. Optionally copy ```application.template.yml``` to ```application.yml``` to change settings (will be .gitignored)
4. Compile and execute the code using ```./gradlew run```
2. Checkout the source using `git clone https://github.com/molgenis/molgenis-service-armadillo.git`
3. Optionally copy `application.template.yml` to `application.yml` to change settings (will be .gitignored)
4. Compile and execute the code using `./gradlew run`

Note: contact MOLGENIS team if you want to contribute and need a testing OIDC config that you can run against localhost.

# Developing Armadillo

We use gradle to build:
* run using ```./gradlew run```
* run tests using ```./gradlew test```
* run using `./gradlew run`
* run tests using `./gradlew test`

We use intellij to develop
* To run or debug in intellij, right click on armadillo/src/main/java/org.molgenis.armdadillo/ArmadilloServiceAppliction and choose 'Run/Debug Armadillo...'
* To run using oidc, create a copy of [application.yml](application.template.yml) in root of your project

We have a swagger-ui to quickly see and test available web services at http://localhost:8080/swagger-ui/

## Components

We have several components

- [Armadillo](./armadillo/src/) source
- [UI](./ui/README.md) readme
- [R](./r/) java integration source
- [docker builds](./docker/) source
- [scripts](./scripts/README.md) migration readme
- [install](./scripts/install/README.md) readme
- [release](./scripts/release/) source
- [ops](./scripts/ops/README.md) readme

## Profile xenon with resourcer whitelisted returns a host.docker.internal error
When developing locally, it might be possible to come across the container error: `Could not resolve host: host.docker.internal`,
especially when developing on a non-supported operating system when resourcer is whitelisted (such as xenon).
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