Merge branch 'master' into test/component_projectexplorer_view

.circleci/config.yml

@@ -7,7 +7,7 @@ version: 2.1
 jobs:
   build:
     docker:
-      - image: eclipse-temurin:17.0.8_7-jdk-jammy
+      - image: eclipse-temurin:17.0.9_9-jdk-jammy
 
     working_directory: ~/repo
     resource_class: large

CONTRIBUTING.md

@@ -0,0 +1,63 @@
+# Contributing to Armadillo
+
+## Running Armadillo from source code
+
+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```
+
+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```
+
+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/ 
+
+## 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). 
+Sadly, the only way around this error is to edit the JAVA source code of Armadillo to include starting with an extra host.
+To enable this feature, you must edit the private method `installImage` of [DockerService.java](https://github.com/molgenis/molgenis-service-armadillo/blob/master/armadillo/src/main/java/org/molgenis/armadillo/profile/DockerService.java) `CreateContainerCmd cmd` from `.withHostConfig(new HostConfig().withPortBindings(portBindings))` to `.withHostConfig(new HostConfig().withPortBindings(portBindings).withExtraHosts("host.docker.internal:host-gateway"))`.
+
+Please note that in order for this change to work, you must use Intellij to run Armadillo or compile the new source code.
+Also, if you already have a xenon container build and running, stop and remove that container.
+
+# Developing DataSHIELD packages in Armadillo
+As package developer will want to push your new packages into a DataSHIELD profile
+
+* You can start Armadillo with defaults as described above; then use admin/admin as authentication
+* to see what profile are available and has been selected:
+```
+curl -u admin:admin http://localhost:8080/profiles
+```
+* to change selected profile 'my-profile':
+```
+curl -X POST http://localhost:8080/select-profile \
+  -H 'Content-Type: application/json' \
+  -d 'default'
+```
+* to install-packages in DataSHIELD current using admin user:
+```
+curl -u admin:admin -v \
+-H 'Content-Type: multipart/form-data' \
+-F "file=@dsBase_6.3.0.tar.gz" \
+-X POST http://localhost:8080/install-package
+```
+* to update whitelist of your current profile:
+```
+curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+```
+* to get whitelist of current profile:
+```
+curl -u admin:admin http://localhost:8080/whitelist
+```

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:17.0.8_7-jdk-focal
+FROM eclipse-temurin:17.0.9_9-jdk-focal
 VOLUME /data
 ARG JAR_FILE
 EXPOSE 8080