Merge pull request #1431 from thehyve/dev

Release version 0.7.29.
thehyve · Aug 25, 2023 · 8f8b06d · 8f8b06d
2 parents b62949c + 5e66302
commit 8f8b06d
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diff --git a/README.adoc b/README.adoc
@@ -2500,7 +2500,7 @@ Create DNS records for the ``keycloak.example.com``, ``fairspace.example.com`` a
 # List available fairspace chart versions
 ~/bin/helm/helm search repo --versions fairspace/fairspace
 # Fetch the fairspace chart
-~/bin/helm/helm pull fairspace/fairspace --version 0.7.28
+~/bin/helm/helm pull fairspace/fairspace --version 0.7.29
 ----
 
 ===== Deploy Keycloak
@@ -2586,7 +2586,7 @@ Create a new deployment (called _release_ in helm terminology) and
 install the Fairspace chart:
 [source, shell]
 ----
-~/bin/helm/helm install fairspace-new fairspace/fairspace --version 0.7.28 --namespace fairspace-new \
+~/bin/helm/helm install fairspace-new fairspace/fairspace --version 0.7.29 --namespace fairspace-new \
 -f /path/to/values.yaml --set-file saturn.vocabulary=/path/to/vocabulary.ttl --set-file saturn.views=/path/to/views.yaml
 ----
 You can pass values files with ``-f`` and provide a file for a specified
@@ -2723,7 +2723,7 @@ jupyterhub:
 To update a deployment using a new chart:
 [source, shell]
 ----
-~/bin/helm/helm upgrade fairspace-new fairspace-0.7.28.tgz
+~/bin/helm/helm upgrade fairspace-new fairspace-0.7.29.tgz
 ----
 With ``helm upgrade`` you can also pass new values files with ``-f``
 and pass files with ``--set-file`` as for ``helm install``.
@@ -3004,9 +3004,8 @@ Pluto keeps track of user sessions, handles the OIDC authentication flow (author
 JWT tokens (validation, refreshing) and redirects to back-end applications.
 
 Pluto is a link:https://spring.io/projects/spring-boot[Java Spring Boot] application,
-using link:https://github.com/Netflix/zuul[Netflix Zuul] as an embedded reverse proxy
-and link:https://bitbucket.org/connect2id/nimbus-jose-jwt[Nimbus JOSE + JWT library] to connect to Keycloak,
-follow the authentication flow and to handle JWT tokens.
+using link:https://github.com/spring-cloud/spring-cloud-gateway[Spring Cloud Gateway] to route APIs
+and, together with link:https://bitbucket.org/connect2id/nimbus-jose-jwt[Nimbus JOSE + JWT library], to connect to Keycloak, follow the authentication flow, handle web sessions and JWT tokens.
 
 === Saturn
 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.7.28
+0.7.29
diff --git a/charts/fairspace/templates/project/configmap-pluto.yaml b/charts/fairspace/templates/project/configmap-pluto.yaml
@@ -12,6 +12,8 @@ data:
         - {{ template "fairspace.url" . }}
 {{ if .Values.pluto.externalDomains }}{{ toYaml .Values.pluto.externalDomains | indent 8 }}{{ end }}
       downstreamServiceHealthUrl: {{ .Values.pluto.backends.saturn | default "http://localhost:8090"}}/api/health/
+      max-file-size: {{ .Values.pluto.maxFileSize }}
+      staticHtmlLocation: /opt/mercury
       oauth2:
         base-url: {{ .Values.external.keycloak.baseUrl }}
         realm: {{ .Values.external.keycloak.realm }}
@@ -41,25 +43,31 @@ data:
         clientSecret: '{{ .Values.external.keycloak.clientSecret }}'
 
     spring:
-      zipkin:
-        enabled: {{ .Values.tracing.enabled }}
-        base-url: {{ .Values.tracing.baseUrl }}
-      servlet:
-        multipart:
-          max-file-size: {{ .Values.pluto.maxFileSize }}
-          max-request-size: {{ .Values.pluto.maxRequestSize }}
-
-    zuul:
-      retryable: false
-      host:
-        connect-timeout-millis: {{ .Values.pluto.connectTimeoutMillis }}
-        socket-timeout-millis: {{ .Values.pluto.socketTimeoutMillis }}
-      routes:
+      web:
+        resources:
+          static-locations: classpath:static,file:/opt/mercury
+      cloud:
+        gateway:
+          routes:
 {{ if .Values.pluto.backends.storageRoutes }}
 {{ toYaml .Values.pluto.backends.storageRoutes | indent 8 }}
 {{ end }}
-        saturn:
-          path: /api/**
-          url: {{ .Values.pluto.backends.saturn | default "http://localhost:8090"}}
-          strip-prefix: false
-      add-proxy-headers: false
+          - id: saturn-post-request-size
+            uri: {{ .Values.pluto.backends.saturn | default "http://localhost:8090/api/" }}
+            predicates:
+            - Method=POST
+            - Path=/api/**
+            filters:
+            - name: RequestSize
+              args:
+                maxSize: {{ .Values.pluto.maxFileSize }}
+          - id: saturn
+            uri: {{ .Values.pluto.backends.saturn | default "http://localhost:8090"}}
+            predicates:
+            - Path=/api/**
+          default-filters:
+            - RemoveRequestHeader=Pragma X-Frame-Options X-Content-Type-Options X-XSS-Protection X-Permitted-Cross-Domain-Policies Origin
+            # Including the ORIGIN header would trigger CORS filtering downstream, but Pluto is already doing the filtering.
+          httpclient:
+            connect-timeout: {{ .Values.pluto.connectTimeoutMillis }}
+            response-timeout: {{ .Values.pluto.responseTimeoutMillis }}
diff --git a/charts/fairspace/templates/project/stateful-set.yaml b/charts/fairspace/templates/project/stateful-set.yaml
@@ -25,6 +25,7 @@ spec:
       containers:
         - name: {{ .Release.Name }}-postgres-database
           image: postgres:15-alpine
+          args: ["-c", "checkpoint_timeout=43200"]
           volumeMounts:
             - name: postgres
               mountPath: /var/lib/postgresql/data

diff --git a/charts/fairspace/values.yaml b/charts/fairspace/values.yaml
@@ -167,11 +167,10 @@ pluto:
   terminationGracePeriodSeconds: 10
   keycloak:
     redirectAfterLogoutUrl:
-  # Zuul timeouts when connecting to upstream services
-  socketTimeoutMillis: 600000  # 10 minutes
+  # Gateway timeouts when connecting to upstream services
+  responseTimeoutMillis: 600000  # 10 minutes
   connectTimeoutMillis: 2000
   maxFileSize: 1GB    # max total size of file(s) that can be uploaded
-  maxRequestSize: 1GB  # max total size of the request (should be > maxFileSize)
   backends:
     storageRoutes:
 

diff --git a/local-development/docker-compose.yml b/local-development/docker-compose.yml
@@ -64,6 +64,7 @@ services:
     volumes:
       - fairspace-postgres-data:/var/lib/postgresql/data
     restart: unless-stopped
+    command: ["postgres", "-c", "checkpoint_timeout=43200"]
     logging:
       driver: ${DOCKER_LOGGING_DRIVER:-journald}
       options:

diff --git a/local-development/fairspace/local-values.yaml b/local-development/fairspace/local-values.yaml
@@ -37,7 +37,6 @@ pluto:
     image: pluto-local
     tag: latest
     pullPolicy: Never
-  socketTimeoutMillis: 600000  # 10 minutes
+  responseTimeoutMillis: 600000  # 10 minutes
   connectTimeoutMillis: 2000
   maxFileSize: 1GB
-  maxRequestSize: 1GB
diff --git a/projects/mercury/configmap-server.yaml b/projects/mercury/configmap-server.yaml
@@ -11,7 +11,7 @@ data:
     config.json: |-
         {
           "urls": {
-            "download": "{{ template "workspace.url" . }}/zuul/api/webdav",
+            "download": "{{ template "workspace.url" . }}/api/webdav",
             "files": "{{ template "storage.url" . }}/api/webdav"
             {{ if ( and .Values.services .Values.services.jupyterhub  ) }}, "jupyterhub": "{{ .Values.services.jupyterhub }}"{{ end }}
             {{ if ( and .Values.services .Values.services.cbioportal  ) }}, "cbioportal": "{{ .Values.services.cbioportal }}"{{ end }}

diff --git a/projects/mercury/src/file/FileAPI.js b/projects/mercury/src/file/FileAPI.js
@@ -40,10 +40,6 @@ class FileAPI {
         this.remoteURL = remoteURL;
     }
 
-    uploadClient() {
-        return createClient('/zuul' + this.remoteURL);
-    }
-
     client() {
         return createClient(this.remoteURL);
     }
@@ -169,7 +165,7 @@ class FileAPI {
             onUploadProgress,
             data: formData
         };
-        return this.uploadClient()
+        return this.client()
             .customRequest(destinationPath, requestOptions)
             .catch(e => {
                 if (e && e.response) {

diff --git a/projects/mercury/src/file/FileBrowser.js b/projects/mercury/src/file/FileBrowser.js
@@ -107,19 +107,12 @@ export const FileBrowser = (props: FileBrowserProperties) => {
     const [overwriteFileCandidateNames, setOverwriteFileCandidateNames] = useState([]);
     const [overwriteFolderCandidateNames, setOverwriteFolderCandidateNames] = useState([]);
     const [currentUpload, setCurrentUpload] = useState({});
-    const [isFolderUpload, setIsFolderUpload] = useState();
 
-    const {
-        getRootProps,
-        getInputProps,
-        isDragActive,
-        isDragAccept,
-        isDragReject,
-        open
-    } = useDropzone({
+    const useFairspaceDropzone = () => useDropzone({
         noClick: true,
         noKeyboard: true,
         multiple: true,
+        useFsAccessApi: false,
         onDropAccepted: (droppedFiles) => {
             const newUpload = {
                 id: generateUuid(),
@@ -144,6 +137,9 @@ export const FileBrowser = (props: FileBrowserProperties) => {
         }
     });
 
+    const fileDropzoneProperties = useFairspaceDropzone();
+    const folderDropzoneProperties = useFairspaceDropzone();
+
     // Deselect all files on history changes
     useEffect(() => {
         const historyListener = history.listen(() => {
@@ -156,13 +152,6 @@ export const FileBrowser = (props: FileBrowserProperties) => {
         // eslint-disable-next-line react-hooks/exhaustive-deps
     }, [history]);
 
-    // A hook to make sure that isFolderUpload state is changed before opening the upload dialog
-    useEffect(() => {
-        if (isFolderUpload !== undefined) {
-            open();
-        }
-    }, [isFolderUpload, open]);
-
     const isParentCollectionDeleted = openedCollection.dateDeleted != null;
     const parentCollectionDeletedRef = useRef(isParentCollectionDeleted);
     useEffect(() => {
@@ -191,19 +180,11 @@ export const FileBrowser = (props: FileBrowserProperties) => {
     }
 
     const uploadFolder = () => {
-        if (isFolderUpload) {
-            open();
-        } else {
-            setIsFolderUpload(true);
-        }
+        folderDropzoneProperties.open();
     };
 
     const uploadFile = () => {
-        if (!isFolderUpload) {
-            open();
-        } else {
-            setIsFolderUpload(false);
-        }
+        fileDropzoneProperties.open();
     };
 
     // A highlighting of a path means only this path would be selected/checked
@@ -300,10 +281,13 @@ export const FileBrowser = (props: FileBrowserProperties) => {
     return (
         <div data-testid="files-view" className={classes.container}>
             <div
-                {...getRootProps()}
-                className={`${classes.dropzone} ${isDragActive && classes.activeStyle} ${isDragAccept && classes.acceptStyle} ${isDragReject && classes.rejectStyle}`}
+                {...fileDropzoneProperties.getRootProps()}
+                className={`${classes.dropzone} ${fileDropzoneProperties.isDragActive && classes.activeStyle} ${fileDropzoneProperties.isDragAccept && classes.acceptStyle} ${fileDropzoneProperties.isDragReject && classes.rejectStyle}`}
             >
-                <input {...getInputProps()} {...(isFolderUpload && {webkitdirectory: ""})} />
+                {/* Since dropzone doesn't support a native folder picker we need to create an input element for both folders and files
+                https://github.com/react-dropzone/react-dropzone/discussions/1157 */}
+                <input {...fileDropzoneProperties.getInputProps({webkitdirectory: undefined})} />
+                <input {...folderDropzoneProperties.getInputProps({webkitdirectory: ""})} />
                 <FileList
                     selectionEnabled={openedCollection.canRead}
                     files={files.map(item => ({...item, selected: selection.isSelected(item.filename)}))}

diff --git a/projects/mercury/src/metadata/common/LinkedDataValuesList.js b/projects/mercury/src/metadata/common/LinkedDataValuesList.js
@@ -128,7 +128,7 @@ export const LinkedDataValuesList = (props: LinkedDataValuesListProps) => {
             key={index}
         >
             <Grid item xs={property.isEditable ? 10 : 12} className={classes.values}>
-                <div style={{overflow: "hidden", textOverflow: "ellipsis", width: "20rem"}}>
+                <div style={{overflow: "hidden", textOverflow: "ellipsis"}}>
                     {
                         columnDefinition.id === LABEL_URI
                             ? <Typography variant="h6">{columnDefinition.getValue(entry, index)}</Typography>

diff --git a/projects/mercury/src/permissions/PermissionCard.js b/projects/mercury/src/permissions/PermissionCard.js
@@ -225,6 +225,7 @@ export const PermissionCard = (props: PermissionCardProperties) => {
         <ListItemText
             primary={camelCaseToWords(collection.accessMode)}
             secondary={descriptionForAccessMode(collection.accessMode)}
+            style={{whiteSpace: "normal"}}
         />
     );
     const showMultipleAccessModes = () => (
@@ -241,6 +242,7 @@ export const PermissionCard = (props: PermissionCardProperties) => {
                         <ListItemText
                             primary={camelCaseToWords(mode)}
                             secondary={descriptionForAccessMode(mode)}
+                            style={{whiteSpace: "normal"}}
                         />
                     </MenuItem>
                 ))}
@@ -249,6 +251,7 @@ export const PermissionCard = (props: PermissionCardProperties) => {
                     .map(unavailableMode => (
                         <MenuItem key={unavailableMode} value={unavailableMode} disabled>
                             <ListItemText
+                                style={{whiteSpace: "normal"}}
                                 primary={camelCaseToWords(unavailableMode)}
                                 secondary={descriptionForAccessMode(unavailableMode)}
                             />
@@ -351,7 +354,7 @@ export const PermissionCard = (props: PermissionCardProperties) => {
             />
             <Collapse in={expanded} timeout="auto" unmountOnExit>
                 <CardContent style={{paddingTop: 0}}>
-                    <div>
+                    <div style={{overflowX: "auto"}}>
                         <List>
                             <ListItem disableGutters>
                                 {renderAccessMode()}

diff --git a/projects/mercury/src/setupProxy.js b/projects/mercury/src/setupProxy.js
@@ -29,7 +29,7 @@ module.exports = (app) => {
     );
 
     // Return 401 Unauthorized for API requests
-    keycloak.redirectToLogin = (request) => !(request.baseUrl.startsWith('/api/') || request.baseUrl.startsWith('/zuul/'));
+    keycloak.redirectToLogin = (request) => !(request.baseUrl.startsWith('/api/'));
 
     app.use(keycloak.middleware({logout: '/logout'}));
     app.use('/dev', keycloak.protect());
@@ -41,11 +41,6 @@ module.exports = (app) => {
         onProxyReq: addToken
     }));
 
-    app.use(createProxyMiddleware('/zuul', {
-        target: 'http://localhost:8080/',
-        onProxyReq: addToken
-    }));
-
     app.use(createProxyMiddleware('/actuator/health', {
         target: 'http://localhost:8080/'
     }));

diff --git a/projects/pluto/build.gradle b/projects/pluto/build.gradle
@@ -1,20 +1,19 @@
 buildscript {
     ext {
-        mockitoVersion = '3.12.0'
+        mockitoVersion = '5.3.1'
     }
 }
 
 plugins {
     id 'java'
-    id 'org.springframework.boot' version '2.7.10'
-    id "io.freefair.lombok" version "6.1.0"
+    id 'org.springframework.boot' version '3.1.0'
+    id "io.freefair.lombok" version '8.0.1'
     id 'application'
     id 'jacoco'
-    //id 'com.github.spotbugs' version '1.6.10'
     id "org.owasp.dependencycheck" version '8.2.1'
+    id 'io.spring.dependency-management' version '1.1.0'
 }
 
-apply plugin: 'io.spring.dependency-management'
 
 group 'nl.fairspace'
 version System.getenv('VERSION') ?: '0.0.1-SNAPSHOT'
@@ -37,31 +36,30 @@ repositories {
 }
 
 ext {
-    springCloudVersion = '2021.0.2'
-    jacksonVersion = '2.14.2'
+    springCloudVersion = '2022.0.3'
+    jacksonVersion = '2.15.2'
 }
 
 jacoco.toolVersion = "0.8.7"
 
 dependencies {
     implementation("com.fasterxml.jackson.core:jackson-annotations:${jacksonVersion}")
-    implementation('javax.validation:validation-api:2.0.1.Final')
-    implementation('org.springframework.boot:spring-boot-starter-web')
-    implementation('org.springframework.cloud:spring-cloud-starter-netflix-zuul:2.2.10.RELEASE')
     implementation('org.springframework.boot:spring-boot-starter-actuator')
+    implementation('org.springframework.cloud:spring-cloud-gateway-mvc')
     implementation('org.springframework.session:spring-session-core')
-    implementation('org.springframework.cloud:spring-cloud-starter-sleuth')
-    implementation('org.springframework.cloud:spring-cloud-sleuth-zipkin')
+    implementation 'io.micrometer:micrometer-tracing-bridge-brave'
+    implementation("org.springframework.cloud:spring-cloud-starter-gateway")
+    implementation('org.springframework.boot:spring-boot-actuator')
 
     implementation 'com.nimbusds:nimbus-jose-jwt:9.31'
-    implementation 'com.nimbusds:oauth2-oidc-sdk:10.7'
+    implementation 'com.nimbusds:oauth2-oidc-sdk:10.9.1'
 
-    testImplementation 'junit:junit:4.12'
+    testImplementation 'junit:junit:4.13.2'
     testImplementation "org.mockito:mockito-core:${mockitoVersion}"
     testImplementation 'org.springframework.boot:spring-boot-starter-test'
     testImplementation 'org.springframework.cloud:spring-cloud-contract-wiremock'
     testImplementation 'org.apache.commons:commons-lang3:3.12.0'
-    testImplementation 'commons-io:commons-io:2.8.0'
+    testImplementation 'commons-io:commons-io:2.12.0'
 
     annotationProcessor "org.springframework.boot:spring-boot-configuration-processor"
 }

diff --git a/projects/pluto/gradle/wrapper/gradle-wrapper.jar b/projects/pluto/gradle/wrapper/gradle-wrapper.jar
diff --git a/projects/pluto/gradle/wrapper/gradle-wrapper.properties b/projects/pluto/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.1-bin.zip
+networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists