Skip to content

Frequently Asked Questions

Docker gives a java.socket error

You might need to enable Docker socket. On Docker desktop you can find that under 'settings' and 'advanced'.

Can I use docker compose to start profiles?

Instead of making Armadillo start/stop DataSHIELD profiles you can also use docker compose. See commented section in docker-compose.yml file.

Can I pass environment or commandline variables instead of application.yml?

Yes, it is standard spring.

Can I run Armadillo with oauth2 config offline?

Yes, you can run in 'offline' profile 

./gradlew run -Dspring.profiles.active=offline

How to run Armadillo version 2?

For armadillo 2.x you can follow instructions for testing we use docker compose. For production environment we are using Ansible

How to run Armadillo as developer?

We develop Armadillo using IntelliJ.

How to build Armadillo

Run following command in the github root: ./gradlew build

To execute in 'dev' run following command in the github root: ./gradlew run

Setting up development tools

This repository uses pre-commit to manage commit hooks. An installation guide can be found here. To install the hooks, run pre-commit install from the root folder of this repository. Now your code will be automatically formatted whenever you commit.

How to change data directory

Data is automatically stored in the data folder in this repository. You can choose another location in application.yml by changing the storage.root-dir setting.

When you run Armadillo locally for the first time, the lifecycle project has not been added to the system metadata yet. To add it automatically, see Application properties. Alternatively you can add it manually:

  • Go to the Swagger UI (http://localhost:8080/swagger-ui/index.html)
  • Go to the PUT /access/projects endpoint
  • Add the project lifecycle

Working with resources in development mode

When developing locally, docker has trouble connecting to localhost. This problem becomes clear when working with resources. Luckily there is a quick fix for the problem. Instead of defining a resource as for example http://localhost:8080/storage/projects/omics/objects/test%2Fgse66351_1.rda, rewrite it to: http://host.docker.internal:8080/storage/projects/omics/objects/test%2Fgse66351_1.rda. Here's some example R code for uploading resources:

## Uploading resources
library(MolgenisArmadillo)
library(resourcer)

token <- armadillo.get_token("http://localhost:8080/")

resGSE1 <- resourcer::newResource(
  name = "GSE66351_1",
  secret = token,
  url = "http://host.docker.internal:8080/storage/projects/omics/objects/test%2Fgse66351_1.rda",
  format = "ExpressionSet"
)

armadillo.login("http://localhost:8080/")
armadillo.upload_resource(project="omics", folder="ewas", resource = resGSE1, name = "GSE66351_1")
And for using them: 
library(DSMolgenisArmadillo)
library(dsBaseClient)

token <- armadillo.get_token("http://localhost:8080/")

builder <- DSI::newDSLoginBuilder()
builder$append(
  server = "local",
  url = "http://localhost:8080/",
  token = token,
  driver = "ArmadilloDriver",
  profile = "uniform",
  resource = "omics/ewas/GSE66351_1"
)

login_data <- builder$build()
conns <- DSI::datashield.login(logins = login_data, assign = TRUE)

datashield.resources(conns = conns)
datashield.assign.resource(conns, resource="omics/ewas/GSE66351_1", symbol="eSet_0y_EUR")
ds.class('eSet_0y_EUR', datasources = conns)
datashield.assign.expr(conns, symbol = "methy_0y_EUR",expr = quote(as.resource.object(eSet_0y_EUR)))