Merge branch 'master' into feat/#809-vanilla-rserve

armadillo/build.gradle

@@ -98,7 +98,7 @@ jacocoTestReport {
 
 spotless {
     java {
-        googleJavaFormat('1.15.0')
+        googleJavaFormat('1.17.0')
     }
 }
 

armadillo/src/main/java/org/molgenis/armadillo/exceptions/InvalidObjectNameException.java

@@ -8,10 +8,10 @@
 @ResponseStatus(BAD_REQUEST)
 public class InvalidObjectNameException extends RuntimeException {
 
-    public InvalidObjectNameException(String objectName) {
-        super(
-                format(
-                        "Object name '%s' is invalid. Object format should be in the following format: folder/file.",
-                        objectName));
-    }
+  public InvalidObjectNameException(String objectName) {
+    super(
+        format(
+            "Object name '%s' is invalid. Object format should be in the following format: folder/file.",
+            objectName));
+  }
 }

armadillo/src/main/java/org/molgenis/armadillo/profile/ProfileScope.java

@@ -11,6 +11,7 @@
 @Component
 public class ProfileScope implements Scope {
   private static final Logger LOGGER = LoggerFactory.getLogger(ProfileScope.class);
+
   /** Contains all profile scoped beans for all profiles */
   private final ConcurrentHashMap<String, Object> scopedBeans = new ConcurrentHashMap<>();
 

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

@@ -104,10 +104,10 @@ public void createLinkedObject(
     }
     try {
       ArmadilloLinkFile armadilloLinkFile =
-              createLinkFileFromSource(sourceProject, sourceObject, variables, linkName, linkProject);
+          createLinkFileFromSource(sourceProject, sourceObject, variables, linkName, linkProject);
       InputStream is = armadilloLinkFile.toStream();
       storageService.save(
-              is, SHARED_PREFIX + linkProject, armadilloLinkFile.getFileName(), APPLICATION_JSON);
+          is, SHARED_PREFIX + linkProject, armadilloLinkFile.getFileName(), APPLICATION_JSON);
     } catch (IllegalArgumentException e) {
       throw new InvalidObjectNameException(linkName);
     }
@@ -230,14 +230,15 @@ private static Workspace toWorkspace(ObjectMetadata item) {
   private void trySaveWorkspace(ArmadilloWorkspace workspace, Principal principal, String id) {
     try {
       storageService.save(
-              workspace.createInputStream(),
-              getUserBucketName(principal),
-              getWorkspaceObjectName(id),
-              APPLICATION_OCTET_STREAM);
+          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("/");
@@ -249,9 +250,9 @@ public void saveWorkspace(InputStream is, Principal principal, String id) {
         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)));
+            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

@@ -7,7 +7,8 @@
 
 public class ArmadilloWorkspace {
   byte[] content;
-  public static final String WORKSPACE_TOO_BIG_ERROR = "Unable to load workspace. Maximum supported workspace size is 2GB";
+  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);

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

@@ -21,7 +21,8 @@ public class ArmadilloLinkFileTest {
   String linkProject = "view-project";
   ArmadilloLinkFile alf = new ArmadilloLinkFile(srcProject, srcObj, vars, linkObj, linkProject);
 
-  @Test void testThrowsIllegalArgumentExceptionWhenInvalidLinkObject() {
+  @Test
+  void testThrowsIllegalArgumentExceptionWhenInvalidLinkObject() {
     try {
       new ArmadilloLinkFile(srcProject, srcObj, vars, "broken", linkProject);
     } catch (IllegalArgumentException e) {

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

@@ -520,11 +520,13 @@ void testSaveWorkspaceReturnsErrorWhenTooBig() {
 
   @Test
   void testSaveWorkspaceReturnsErrorWhenBiggerThan2Gbs() {
-    when(storageService.getWorkSpace(is)).thenThrow(new StorageException(ArmadilloWorkspace.WORKSPACE_TOO_BIG_ERROR));
+    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());
+      assertEquals(
+          "Unable to save workspace. Maximum supported workspace size is 2GB", e.getMessage());
     }
   }
 
@@ -617,10 +619,10 @@ void testCreateLinkedObjecInvalidLinkObj() {
     mockExistingObject(SHARED_GECKO, "1_0_release_1_1/gecko.parquet");
     when(storageService.listBuckets()).thenReturn(List.of(SHARED_DIABETES, SHARED_GECKO));
     assertThrows(
-            InvalidObjectNameException.class,
-            () ->
-                    armadilloStorage.createLinkedObject(
-                            "gecko", "1_0_release_1_1/gecko", "my_link", "diabetes", "a,b,c"));
+        InvalidObjectNameException.class,
+        () ->
+            armadilloStorage.createLinkedObject(
+                "gecko", "1_0_release_1_1/gecko", "my_link", "diabetes", "a,b,c"));
   }
 
   @Test

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

@@ -35,7 +35,7 @@ void testGetByteOfInputStreamThrowsMemoryError() throws IOException {
     when(isMock.read(any(byte[].class))).thenThrow(OutOfMemoryError.class);
     try {
       new ArmadilloWorkspace(isMock);
-    } catch(StorageException e) {
+    } catch (StorageException e) {
       assertEquals(ArmadilloWorkspace.WORKSPACE_TOO_BIG_ERROR, e.getMessage());
     }
   }

r/build.gradle

@@ -76,7 +76,7 @@ jacocoTestReport {
 
 spotless {
     java {
-        googleJavaFormat('1.15.0')
+        googleJavaFormat('1.17.0')
     }
 }
 

ui/src/App.vue

@@ -14,14 +14,20 @@
               {{ diskSpaceMessage }}
             </Alert>
             <Alert v-if="isUnauthorised" type="warning" :dismissible="false">
-              You are logged in, but you don't have permission to access the Armadillo user interface.
+              You are logged in, but you don't have permission to access the
+              Armadillo user interface.
               <div>
                 Don't worry, you can still do your research using the R client.
-                If you believe you should have permission to access this user interface, please contact an administrator.
+                If you believe you should have permission to access this user
+                interface, please contact an administrator.
               </div>
             </Alert>
             {{ errorMessage }}
-            <Tabs v-if="username && !isUnauthorised" :menu="tabs" :icons="tabIcons" />
+            <Tabs
+              v-if="username && !isUnauthorised"
+              :menu="tabs"
+              :icons="tabIcons"
+            />
           </div>
           <Login @loginEvent="reloadUser" v-else />
         </div>
@@ -36,10 +42,20 @@ import Tabs from "@/components/Tabs.vue";
 import Login from "@/views/Login.vue";
 import Alert from "@/components/Alert.vue";
 import { defineComponent, onMounted, ref, Ref } from "vue";
-import { getPrincipal, getVersion, logout, getFreeDiskSpace, getPermissions } from "@/api/api";
+import {
+  getPrincipal,
+  getVersion,
+  logout,
+  getFreeDiskSpace,
+  getPermissions,
+} from "@/api/api";
 import { useRouter } from "vue-router";
 import { ApiError } from "@/helpers/errors";
-import { diskSpaceBelowThreshold, convertBytes, isEmpty } from "@/helpers/utils";
+import {
+  diskSpaceBelowThreshold,
+  convertBytes,
+  isEmpty,
+} from "@/helpers/utils";
 
 export default defineComponent({
   name: "ArmadilloPortal",
@@ -77,8 +93,7 @@ export default defineComponent({
             if (error.cause == 403) {
               isUnauthorised.value = true;
             }
-          })
-              
+          });
         })
         .catch((error: ApiError) => {
           if (error.cause === 401) {

ui/src/api/api.ts

@@ -17,7 +17,11 @@ import {
   Metrics,
 } from "@/types/api";
 
-import { ObjectWithStringKey, StringArray, ListOfObjectsWithStringKey } from "@/types/types";
+import {
+  ObjectWithStringKey,
+  StringArray,
+  ListOfObjectsWithStringKey,
+} from "@/types/types";
 import { APISettings } from "./config";
 
 export async function get(url: string, auth: Auth | undefined = undefined) {
@@ -199,7 +203,7 @@ export async function getProjects(): Promise<Project[]> {
 }
 
 export function getPermissions(): Promise<ListOfObjectsWithStringKey> {
-  return get("/access/permissions")
+  return get("/access/permissions");
 }
 
 export async function getFiles(): Promise<RemoteFileInfo[]> {

ui/src/components/DataPreviewTable.vue

@@ -17,7 +17,7 @@
         <!-- for each value in row -->
         <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 ) }}..
+            {{ value.toString().slice(0, tableHeader[index].length - 2) }}..
           </span>
           <span v-else>
             {{ value }}

ui/src/components/FormValidation.vue

@@ -1,8 +1,11 @@
 <template>
-  <div :class="isValidated && validationCondition ? 'invalid-field' : ''" class="p-1">
+  <div
+    :class="isValidated && validationCondition ? 'invalid-field' : ''"
+    class="p-1"
+  >
     <slot></slot>
     <div v-if="isValidated && validationCondition" class="feedback">
-      {{  invalidMessage }}
+      {{ invalidMessage }}
     </div>
   </div>
 </template>
@@ -15,17 +18,17 @@ export default defineComponent({
   props: {
     isValidated: {
       type: Boolean,
-      default: false
+      default: false,
     },
     validationCondition: {
       type: Boolean,
-      required: true
+      required: true,
     },
     invalidMessage: {
       type: String,
-      required: true
-    }
-  }
+      required: true,
+    },
+  },
 });
 </script>
 
@@ -38,9 +41,8 @@ export default defineComponent({
 }
 
 .feedback {
-  color:  rgb(220, 53, 69);
+  color: rgb(220, 53, 69);
   font-style: italic;
   font-size: 0.9rem;
 }
-
-</style>
+</style>