Merge branch 'master' into feat/previews-to-aks

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))

docker/ci/docker-compose.yml

@@ -29,9 +29,3 @@ services:
     image: datashield/rock-dolomite-xenon:latest
     environment:
       DEBUG: "TRUE"
-
-  rock:
-    hostname: rock
-    image: datashield/rock-base:latest
-    environment:
-      DEBUG: "TRUE"

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 [email protected]
 ## 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,

scripts/upgrade/requirements.txt

@@ -1,12 +1,12 @@
 -i https://pypi.org/simple
 argon2-cffi==23.1.0; python_version >= '3.7'
 argon2-cffi-bindings==21.2.0; python_version >= '3.6'
-certifi==2024.2.2; python_version >= '3.6'
+certifi==2024.7.4; python_version >= '3.6'
 cffi==1.16.0; python_version >= '3.8'
 charset-normalizer==3.3.2; python_full_version >= '3.7.0'
 deprecated==1.2.14; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 fusionauth-client==1.49.1
-idna==3.6; python_version >= '3.5'
+idna==3.7; python_version >= '3.5'
 minio==7.2.5
 numpy==1.24.4; python_version >= '3.8'
 pandas==2.0.3; python_version >= '3.8'
@@ -19,5 +19,5 @@ simple-term-menu==1.6.4; python_version ~= '3.5'
 six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 typing-extensions==4.10.0; python_version >= '3.8'
 tzdata==2024.1; python_version >= '2'
-urllib3==2.2.1; python_version >= '3.8'
+urllib3==2.2.2; python_version >= '3.8'
 wrapt==1.16.0; python_version >= '3.6'

ui/package.json

@@ -12,19 +12,19 @@
   },
   "dependencies": {
     "@popperjs/core": "2.11.8",
-    "bootstrap": "5.3.2",
+    "bootstrap": "5.3.3",
     "bootstrap-icons": "1.11.3",
     "vue": "3.3.8",
     "vue-router": "^4.0.13"
   },
   "devDependencies": {
-    "@babel/core": "7.23.7",
-    "@babel/preset-typescript": "7.23.3",
-    "@types/jest": "29.5.12",
+    "@babel/core": "7.24.5",
+    "@babel/preset-typescript": "7.24.1",
+    "@types/jest": "29.5.13",
     "@types/node": "20.16.5",
     "@types/vue": "^2.0.0",
     "@vitejs/plugin-vue": "4.4.1",
-    "@vue/test-utils": "2.4.5",
+    "@vue/test-utils": "2.4.6",
     "@vue/vue3-jest": "29.2.6",
     "babel-jest": "29.7.0",
     "jest": "29.7.0",
@@ -36,6 +36,6 @@
     "ts-node": "10.9.2",
     "tslib": "2.6.2",
     "typescript": "4.9.5",
-    "vite": "4.5.2"
+    "vite": "4.5.3"
   }
 }

ui/src/components/ColumnNamesPreview.vue

@@ -0,0 +1,42 @@
+<template>
+  <div>
+    <button
+      type="button"
+      class="btn btn-secondary"
+      @click="toggleColumnNames()"
+    >
+      {{ buttonName }} <i class="bi bi-chevron-down" v-if="!isCollapsed"></i>
+      <i class="bi bi-chevron-up" v-else></i>
+    </button>
+    <div class="fst-italic text-secondary" v-show="isCollapsed">
+      {{ columnNamesString }}
+    </div>
+  </div>
+</template>
+
+<script lang="ts">
+import { defineComponent } from "vue";
+
+export default defineComponent({
+  name: "ColumnNamesPreview",
+  props: {
+    columnNames: { type: Array, required: true },
+    buttonName: String,
+  },
+  data() {
+    return {
+      isCollapsed: false,
+    };
+  },
+  computed: {
+    columnNamesString() {
+      return this.columnNames.join(", ");
+    },
+  },
+  methods: {
+    toggleColumnNames() {
+      this.isCollapsed = !this.isCollapsed;
+    },
+  },
+});
+</script>

ui/src/components/SimpleTable.vue → ui/src/components/DataPreviewTable.vue

@@ -9,26 +9,19 @@
         <th scope="col" v-for="key in tableHeader" :key="key">
           {{ key }}
         </th>
-        <!-- Not required if there are not at least 11 columns -->
-        <th v-if="nCols > 10" scope="col">...</th>
       </tr>
     </thead>
     <tbody class="table-group-divider">
       <!-- for each row-->
       <tr v-for="(row, index) in dataToPreview" :key="index">
         <!-- for each value in row -->
-        <td v-for="(value, key) in row" :key="key">
-          {{ value }}
-        </td>
-        <!-- Will display the "+ x more" if 11 or more columns are present, else hides the column entirely -->
-        <td rowspan="10" v-if="index === 0 && nCols > 10" class="fst-italic">
-          {{ `+ ${nCols - 10} more` }}
-        </td>
-      </tr>
-      <tr class="text-end fst-italic">
-        <!-- Same goes for rows, only display when there are at least 11 or more rows -->
-        <td colspan="11" v-if="nRows > 10">
-          {{ `+ ${nRows - 10} more rows` }}
+        <td v-for="(value, key, index) in row" :key="key">
+          <span v-if="value.toString().length > tableHeader[index].length">
+            {{ value.toString().slice(0, tableHeader[index].length - 2 ) }}..
+          </span>
+          <span v-else>
+            {{ value }}
+          </span>
         </td>
       </tr>
     </tbody>
@@ -41,7 +34,7 @@ import { defineComponent, PropType } from "vue";
 import { isIntArray, transformTable, truncate } from "@/helpers/utils";
 
 export default defineComponent({
-  name: "SimpleTable",
+  name: "DataPreviewTable",
   props: {
     data: {
       type: Array as PropType<{ [key: string]: string }[]>,
@@ -55,10 +48,6 @@ export default defineComponent({
       type: Number,
       required: true,
     },
-    nCols: {
-      type: Number,
-      required: true,
-    },
   },
   computed: {
     maxNumberCharacters() {

ui/src/types/types.d.ts

@@ -57,6 +57,7 @@ export type ProjectsExplorerData = {
   selectedFolder: string;
   createLinkFromTarget: boolean;
   createLinkFromSrc: boolean;
+  columnNames: Array<string>;
 };
 
 export type ProjectsData = {