Merge branch 'master' into feat/preview-col-names

.circleci/config.yml

@@ -9,7 +9,7 @@ version: 2.1
 jobs:
   build:
     docker:
-      - image: eclipse-temurin:17.0.10_7-jdk-jammy
+      - image: eclipse-temurin:17.0.12_7-jdk-jammy
 
     working_directory: ~/repo
     resource_class: large

Dockerfile

@@ -1,4 +1,4 @@
-FROM --platform=linux/amd64 eclipse-temurin:17.0.10_7-jdk-focal
+FROM --platform=linux/amd64 eclipse-temurin:17.0.12_7-jdk-focal
 VOLUME /data
 VOLUME /config
 VOLUME /logs

armadillo/build.gradle

@@ -46,7 +46,7 @@ dependencies {
     //other
     implementation 'org.rosuda.REngine:REngine:2.1.0'
     implementation 'org.rosuda.REngine:Rserve:1.8.1'
-    implementation 'io.swagger.core.v3:swagger-annotations:2.2.20'
+    implementation 'io.swagger.core.v3:swagger-annotations:2.2.23'
     implementation 'com.google.auto.value:auto-value-annotations:1.10.4'
     implementation 'org.obiba.datashield:ds4j-core:2.1.0'
     implementation 'org.obiba.datashield:ds4j-r:2.1.0'

armadillo/src/main/java/org/molgenis/armadillo/info/RProcessEndpoint.java

@@ -15,6 +15,8 @@
 import org.springframework.boot.actuate.endpoint.annotation.ReadOperation;
 import org.springframework.stereotype.Component;
 
+import static org.molgenis.armadillo.security.RunAs.runAsSystem;
+
 @Component
 @Endpoint(id = "rserveProcesses")
 public class RProcessEndpoint {
@@ -41,7 +43,7 @@ public List<REnvironment> getRServeEnvironments() {
 
   <T> T doWithConnection(String environmentName, Function<RServerConnection, T> action) {
     var environment =
-        profileService.getAll().stream()
+            runAsSystem(profileService::getAll).stream()
             .filter(it -> environmentName.equals(it.getName()))
             .map(ProfileConfig::toEnvironmentConfigProps)
             .findFirst()

armadillo/src/main/java/org/molgenis/armadillo/security/AuthConfig.java

@@ -75,6 +75,7 @@ protected SecurityFilterChain oauthAndBasic(HttpSecurity http) throws Exception
                     "/v3/**",
                     "/swagger-ui/**",
                     "/ui/**",
+                    "/actuator/prometheus",
                     "/swagger-ui.html")
                 .permitAll()
                 .requestMatchers(EndpointRequest.to(InfoEndpoint.class, HealthEndpoint.class))

armadillo/src/main/java/org/molgenis/armadillo/storage/ArmadilloStorageService.java

@@ -223,28 +223,34 @@ private static Workspace toWorkspace(ObjectMetadata item) {
         .build();
   }
 
+  private void trySaveWorkspace (ArmadilloWorkspace workspace, Principal principal, String id) {
+    try {
+      storageService.save(
+              workspace.createInputStream(),
+              getUserBucketName(principal),
+              getWorkspaceObjectName(id),
+              APPLICATION_OCTET_STREAM);
+    } catch (StorageException e) {
+      throw new StorageException(e);
+    }
+  }
   public void saveWorkspace(InputStream is, Principal principal, String id) {
     // Load root dir
     File drive = new File("/");
     long usableSpace = drive.getUsableSpace();
-
-    ArmadilloWorkspace workspace = storageService.getWorkSpace(is);
-    long fileSize = workspace.getSize();
-    if (usableSpace > fileSize * 2L) {
-      try {
-        storageService.save(
-            workspace.createInputStream(),
-            getUserBucketName(principal),
-            getWorkspaceObjectName(id),
-            APPLICATION_OCTET_STREAM);
-      } catch (StorageException e) {
-        throw new StorageException(e);
+    try {
+      ArmadilloWorkspace workspace = storageService.getWorkSpace(is);
+      long fileSize = workspace.getSize();
+      if (usableSpace > fileSize * 2L) {
+        trySaveWorkspace(workspace, principal, id);
+      } else {
+        throw new StorageException(
+                format(
+                        "Can't save workspace: workspace too big (%s), not enough space left on device. Try to make your workspace smaller and/or contact the administrator to increase diskspace.",
+                        getHumanReadableByteCount(fileSize)));
       }
-    } else {
-      throw new StorageException(
-          format(
-              "Can't save workspace: workspace too big (%s), not enough space left on device. Try to make your workspace smaller and/or contact the administrator to increase diskspace.",
-              getHumanReadableByteCount(fileSize)));
+    } catch (StorageException e) {
+      throw new StorageException(e.getMessage().replace("load", "save"));
     }
   }
 

armadillo/src/main/java/org/molgenis/armadillo/storage/ArmadilloWorkspace.java

@@ -1,13 +1,13 @@
 package org.molgenis.armadillo.storage;
 
 import java.io.ByteArrayInputStream;
-import java.io.IOException;
 import java.io.InputStream;
 import org.apache.commons.io.IOUtils;
 import org.molgenis.armadillo.exceptions.StorageException;
 
 public class ArmadilloWorkspace {
   byte[] content;
+  public static final String WORKSPACE_TOO_BIG_ERROR = "Unable to load workspace. Maximum supported workspace size is 2GB";
 
   public ArmadilloWorkspace(InputStream is) {
     content = toByteArray(is);
@@ -16,8 +16,10 @@ public ArmadilloWorkspace(InputStream is) {
   private byte[] toByteArray(InputStream is) {
     try {
       return IOUtils.toByteArray(is);
-    } catch (IOException e) {
-      throw new StorageException("Unable to read workspace");
+    } catch (OutOfMemoryError e) {
+      throw new StorageException(WORKSPACE_TOO_BIG_ERROR);
+    } catch (Exception e) {
+      throw new StorageException("Unable to load workspace, because: " + e);
     }
   }
 

armadillo/src/test/java/org/molgenis/armadillo/storage/ArmadilloStorageServiceTest.java

@@ -518,6 +518,16 @@ void testSaveWorkspaceReturnsErrorWhenTooBig() {
         StorageException.class, () -> armadilloStorage.saveWorkspace(is, principal, "test"));
   }
 
+  @Test
+  void testSaveWorkspaceReturnsErrorWhenBiggerThan2Gbs() {
+    when(storageService.getWorkSpace(is)).thenThrow(new StorageException(ArmadilloWorkspace.WORKSPACE_TOO_BIG_ERROR));
+    try {
+      armadilloStorage.saveWorkspace(is, principal, "test");
+    } catch (StorageException e) {
+      assertEquals("Unable to save workspace. Maximum supported workspace size is 2GB", e.getMessage());
+    }
+  }
+
   @Test
   void testSaveWorkspaceChecksBucketName() {
     ArmadilloWorkspace workspaceMock = mock(ArmadilloWorkspace.class);

armadillo/src/test/java/org/molgenis/armadillo/storage/ArmadilloWorkspaceTest.java

@@ -28,4 +28,15 @@ void testGetByteOfInputStreamThrowsError() throws IOException {
     when(isMock.read(any(byte[].class))).thenThrow(IOException.class);
     assertThrows(StorageException.class, () -> new ArmadilloWorkspace(isMock));
   }
+
+  @Test
+  void testGetByteOfInputStreamThrowsMemoryError() throws IOException {
+    InputStream isMock = mock(InputStream.class);
+    when(isMock.read(any(byte[].class))).thenThrow(OutOfMemoryError.class);
+    try {
+      new ArmadilloWorkspace(isMock);
+    } catch(StorageException e) {
+      assertEquals(ArmadilloWorkspace.WORKSPACE_TOO_BIG_ERROR, e.getMessage());
+    }
+  }
 }

docs/minor-release-update.md

@@ -0,0 +1,140 @@
+# Minor Version Upgrade Manual: Procedures for y.z Releases
+
+> Note: This manual is intended for minor version updates within the latest major release. For example, you can use it to update from version 4.1 to 4.7.1. For upgrading to a new major version, please refer to the specific manuals dedicated to major version upgrades.
+
+## Check latest version
+
+For the latest 4.y.z release check https://github.com/molgenis/molgenis-service-armadillo/releases/latest. This will redirect to a v4.y.z page.
+
+# Updating Armadillo
+
+### 1. Stop docker containers
+
+First, log in to the Armadillo UI and navigate to the Profiles tab. Now, click 'Stop' for each profile listed.
+
+Next, stop any unnecessary containers.
+
+The commands provided are indicative, so adjust them as needed.
+
+```bash
+# should return empty list (i.e. default, xenon, rock)
+docker container list
+
+# remove containers not needed
+docker container stop <id>
+```
+
+## 2. Download required files
+
+Make a note of the version number ie. `v4.7.1` as you need to download some files from the terminal using the update script.
+
+### 2.1 Update script
+
+You need to be root user.
+
+```bash
+cd /root
+
+# Make sure to change the versions number v4.y.z
+mkdir v4.y.z
+cd v4.y.z
+
+# Check directory location
+pwd
+```
+
+```bash
+# Change the version number v4.y.z then run command
+wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/v4.y.z/scripts/install/armadillo-check-update.sh
+```
+
+Make the script runnable
+```bash
+chmod u+x armadillo-check-update.sh
+```
+
+### 2.2 Run update script
+
+You can run the following script to download the new Armadillo version.
+
+> The output could help us to help you fix problems.
+
+```bash
+# Change the version number v4.y.z
+./armadillo-check-update.sh 4.y.z
+```
+
+Once the script has completed, you can verify that the Armadillo JAR file has been downloaded by checking the directory:
+
+```bash
+# See all jar files on your system
+ls -ltr /usr/share/armadillo/application/
+```
+
+### 3. Make backup of system config
+
+```bash
+# Still in the correct directory? (`/root/v4.y.z`)
+pwd
+```
+
+We make a backup into the same `v4.y.z` directory but that is not strictly needed.
+
+```bash
+cp -r /usr/share/armadillo/data/system ./
+```
+
+should result in:
+
+```bash
+ls system/
+# access.json  profiles.json
+```
+
+## 4. Restart application using new version
+
+Armadillo has not yet been updated, follow the following steps to do so:
+
+### 4.1 Stop Armadillo
+
+```bash
+systemctl stop armadillo
+```
+
+### 4.2 Link new version
+
+```bash
+# List application files
+ls -l /usr/share/armadillo/application/
+
+# Remove the linked file
+rm /usr/share/armadillo/application/armadillo.jar
+
+# Attach new linked file and dont forget to change the version number v4.y.z
+ln -s /usr/share/armadillo/application/armadillo-4.y.z.jar /usr/share/armadillo/application/armadillo.jar
+
+# Check result
+ls -l /usr/share/armadillo/application/
+```
+
+### 4.3 Restart Armadillo
+
+```bash
+systemctl start armadillo
+systemctl status armadillo
+```
+
+## 5. Log on to the UI
+
+Go to your armadillo website. Is the version in the left top corner updated? This means the update was successful. We're
+almost finished. 
+
+## 6. Start profiles
+
+Login into the website and go to the profiles tab. Now you can start all the profiles again.
+
+Everything should now be working correctly. You can try and login to your server via the central analysis server, using
+the `DSMolgenisArmadillo` (2.0.5 or up) package to test. 
+
+Enjoy =)
+Team Armadillo

docs/ops/installing.md

@@ -47,6 +47,12 @@ The values needed are:
 
 You need a SSL certificate to configuring the front-end proxy and make the browser use **https** before putting data on the server.
 
+If SELinux is enabled, run the following command to ensure that the application can connect to required services:
+
+```bash
+setsebool -P httpd_can_network_connect on
+```
+
 ## Installing Armadillo as service
 
 We run Armadillo in production as a Linux service on Ubuntu, ensuring it gets restarted when the server is rebooted. You might be able to reproduce also on CentOS (using yum instead of apt).
@@ -184,4 +190,4 @@ For questions on other linux release you can email molgenis-operations@umcg.nl
 ## What's next?
 
 * [For the server owner or data manager who need to put data on to the server](https://molgenis.github.io/molgenis-r-armadillo/)
-* [For the researcher who want to start analyzing the data on the server](https://molgenis.github.io/molgenis-r-datashield/)
+* [For the researcher who want to start analyzing the data on the server](https://molgenis.github.io/molgenis-r-datashield/)

docs/ui.md

@@ -206,7 +206,7 @@ By default, some fields will be set. Please update them to install the correct p
 
 Possible images can be found on [dockerhub](https://hub.docker.com/search?q=datashield%2Farmadillo-rserver). We
 recommend selecting one of the
-[DataSHIELD standard profiles](https://www.datashield.org/help/standard-profiles-and-plaforms). The image name of those
+[DataSHIELD standard profiles](https://wiki.datashield.org/en/opmanag/standard-profiles-and-platforms). The image name of those
 profiles can be found on the dockerhub link above.
 
 Although the default `port` setting should find an available port, please keep in mind that the port has to be unique,

r/build.gradle

@@ -35,6 +35,7 @@ dependencies {
     implementation 'com.google.auto.value:auto-value-annotations:1.10.4'
     implementation 'org.apache.commons:commons-text:1.11.0'
     implementation 'org.json:json:20240303'
+    implementation 'org.apache.httpcomponents.client5:httpclient5:5.3.1'
 
     //test
     testImplementation('org.springframework.boot:spring-boot-starter-test') {