Refactoring/fairspc 82

.github/workflows/build_and_upload_on_push_to_dev.yaml

@@ -76,10 +76,10 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: Set Node.js 18.x
-        uses: actions/setup-node@v3
+      - name: Set Node.js 22.x
+        uses: actions/setup-node@v4
         with:
-          node-version: 18.x
+          node-version: 22.x
 
       - name: Set deployment version
         env:

.github/workflows/build_on_pull_request.yaml

@@ -54,10 +54,10 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: Set Node.js 18.x
+      - name: Set Node.js 22.x
         uses: actions/setup-node@v4
         with:
-          node-version: 18.x
+          node-version: 22.x
 
       - name: Log details
         run: |

README.adoc

@@ -2238,10 +2238,10 @@ The data models for these metadata are defined using the {SHACL}[Shapes Constrai
 * The customisable data model includes the custom (shared)
   metadata entities, custom controlled vocabulary types,
   and custom properties of the system entities.
-  The default custom data model is defined in link:projects/saturn/vocabulary.ttl[vocabulary.ttl].
+  The default custom data model is defined in link:projects/saturn/src/main/resources/vocabulary.ttl[vocabulary.ttl].
   This data model can be overriden by a data more suitable for your organisation.
 
-A schematic overview of the default data model in link:projects/saturn/vocabulary.ttl[vocabulary.ttl]:
+A schematic overview of the default data model in link:projects/saturn/src/main/resources/vocabulary.ttl[vocabulary.ttl]:
 
 image:docs/images/diagrams/CDR data model.png[CDR data model]
 
@@ -2462,8 +2462,8 @@ use `--set-file` option:
 +
 This should also restart the Saturn pod. If not, trigger the restart manually.
 +
-For local development - replace vocabulary file in link:projects/saturn/vocabulary.ttl[projects/saturn/vocabulary.ttl]
-and views configuration in link:projects/saturn/views.ttl[projects/saturn/views.ttl].
+For local development - replace vocabulary file in link:projects/saturn/src/main/resources/vocabulary.ttl[vocabulary.ttl]
+and views configuration in link:projects/saturn/src/main/resources/views.yaml[views.yaml].
 Restart Saturn run.
 +
 . Load data for new entities or properties.
@@ -2474,7 +2474,7 @@ Restart Saturn run.
 
 For controlled vocabulary types, e.g., _Gender_ and _Species_ in the example, you should insert the allowed values in the database by uploading
 a taxonomies file using the <<RDF metadata>> API.
-An example taxonomy is in link:projects/saturn/taxonomies.ttl[taxonomies.ttl].
+An example taxonomy is in link:projects/saturn/src/main/resources/taxonomies.ttl[taxonomies.ttl].
 
 It is preferred to use existing standard taxonomies and labels.
 If that is not possible, please define your own namespaces for
@@ -2526,7 +2526,7 @@ ncbitaxon:10090 a example:Species ;
 
 For the metadata pages in the user interface, a view configuration needs to be created
 that specifies the tables and columns.
-An example can be found in link:projects/saturn/views.yaml[views.yaml]
+An example can be found in link:projects/saturn/src/main/resources/views.yaml[views.yaml]
 
 
 
@@ -3233,14 +3233,14 @@ and, together with link:https://bitbucket.org/connect2id/nimbus-jose-jwt[Nimbus
 The heart of Fairspace, back-end application handling all the logic and connection to the storages.
 Data repository and catalog.
 
-Saturn is served as link:https://jena.apache.org/documentation/fuseki2/[Apache Jena Fuseki SPARQL] server,
-embedded into link:https://www.eclipse.org/jetty/[Jetty] Web server.
+Saturn is also a link:https://spring.io/projects/spring-boot[Java Spring Boot] application with embedded Tomcat web server.
 
 Saturn uses link:https://jena.apache.org/documentation/rdf/[Apache Jena RDF] for handling RDF graphs,
 serialisation of triples and TDB triple store connection.
 All data within Fairspace, except to uploaded files and logs, are stored in Apache Jena RDF database.
 
-For security, Saturn is integrated with Keycloak using link:https://www.keycloak.org/docs/latest/securing_apps/#_jetty9_adapter[Keycloak Jetty client adapter].
+Saturn is secured using OAuth2 with Keycloak, integrated with Spring Boot and
+link:https://docs.spring.io/spring-security/reference/servlet/oauth2/[Spring Security].
 It enables user authentication with access tokens.
 
 Saturn is also responsible for authorization of users in Fairspace - it includes user access validators

charts/fairspace/templates/project/configmap-pluto.yaml

@@ -11,7 +11,7 @@ data:
       domains:
         - {{ 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/
+      downstreamServiceHealthUrl: {{ .Values.pluto.backends.saturn | default "http://localhost:8091"}}/actuator/health/
       max-file-size: {{ .Values.pluto.maxFileSize }}
       staticHtmlLocation: /opt/mercury
       oauth2:

charts/fairspace/templates/project/configmap-saturn.yaml

@@ -7,37 +7,71 @@ metadata:
     {{- include "fairspace.labels" . | nindent 4 }}
 data:
   application.yaml: |-
-    port: 8090
-    livenessPort: 8091
-    publicUrl: {{ template "fairspace.url" . }}
-    jena:
-      metadataBaseIRI: http://{{ .Values.fairspace.ingress.domain }}/iri/
-      datasetPath: "/data/saturn/db"
-      storeParams:
-{{ toYaml .Values.saturn.storeParams | indent 8 }}
-      transactionLogPath: "/data/saturn/files/log"
-      bulkTransactions: {{ .Values.saturn.bulkTransactions }}
-    auth:
-      authServerUrl: {{ .Values.external.keycloak.managementUrl | default .Values.external.keycloak.baseUrl }}/
+    server:
+      port: 8090
+      servlet:
+        context-path: /api
+
+    spring:
+      security:
+        oauth2:
+          resourceserver:
+            jwt:
+              issuer-uri: {{ .Values.external.keycloak.baseUrl }}/realms/fairspace
+              jwk-set-uri: {{ .Values.external.keycloak.baseUrl }}/realms/fairspace/protocol/openid-connect/certs
+      servlet:
+        multipart:
+          max-file-size: 2GB
+          max-request-size: 2GB
+      http:
+        multipart:
+          enabled: true
+
+    keycloak:
+      auth-server-url: {{ .Values.external.keycloak.managementUrl | default .Values.external.keycloak.baseUrl }}/
       realm: {{ .Values.external.keycloak.realm }}
-      clientId: {{ .Values.external.keycloak.clientId }}
-      enableBasicAuth: {{ .Values.saturn.auth.enableBasicAuth }}
-      superAdminUser: {{ .Values.external.keycloak.superAdminUser | default (printf "organisation-admin-%s" .Values.external.keycloak.realm ) }}
+      client-id: {{ .Values.external.keycloak.clientId }}
+      super-admin-user: {{ .Values.external.keycloak.superAdminUser | default (printf "organisation-admin-%s" .Values.external.keycloak.realm ) }}
 {{ if .Values.saturn.auth.defaultUserRoles }}
-      defaultUserRoles:
+      default-user-roles:
 {{ toYaml .Values.saturn.auth.defaultUserRoles | indent 8 }}
 {{ end }}
-    webDAV:
-      blobStorePath: "/data/saturn/files/blobs"
-    viewDatabase:
-      enabled: true
-      mvRefreshOnStartRequired: {{ .Values.saturn.mvRefreshOnStartRequired }}
-    features:
-{{ toYaml .Values.fairspace.features | indent 6 }}
+
+    jwt:
+      auth:
+        converter:
+          resource-id: {{ .Values.external.keycloak.clientId }}
+          principal-attribute: preferred_username
+
+    application:
+      publicUrl: {{ template "fairspace.url" . }}
+      jena:
+        metadataBaseIRI: http://{{ .Values.fairspace.ingress.domain }}/iri/
+        datasetPath: "/data/saturn/db"
+        storeParams:
+{{ toYaml .Values.saturn.storeParams | indent 10 }}
+        transactionLogPath: "/data/saturn/files/log"
+        bulkTransactions: {{ .Values.saturn.bulkTransactions }}
+
+      webdav:
+        blobStorePath: "/data/saturn/files/blobs"
 {{ if has "ExtraStorage" .Values.fairspace.features }}
-    extraStorage:
-      blobStorePath: "/data/saturn/extrafiles/blobs"
+        extraStorage:
+          blobStorePath: "/data/saturn/extrafiles/blobs"
+          defaultRootCollections:
+            - "analysis-export"
 {{ end }}
+      view-database:
+        enabled: true
+        url: "jdbc:postgresql://localhost:5432/fairspace"
+        mvRefreshOnStartRequired: {{ .Values.saturn.mvRefreshOnStartRequired }}
+        username: fairspace
+        autoCommitEnabled: false
+        maxPoolSize: 50
+        connectionTimeout: 1000
+        password: fairspace
+      features:
+{{ toYaml .Values.fairspace.features | indent 8 }}
 
   vocabulary.ttl: |
 {{ if .Values.saturn.vocabulary -}}

charts/fairspace/templates/project/stateful-set.yaml

@@ -100,16 +100,16 @@ spec:
 {{- end }}
           livenessProbe:
             httpGet:
-              path:  /liveness
+              path:  /actuator/health/liveness
               port: 8091
             initialDelaySeconds: {{ .Values.saturn.livenessProbe.initialDelaySeconds }}
             periodSeconds: {{ .Values.saturn.livenessProbe.periodSeconds }}
             successThreshold: {{ .Values.saturn.livenessProbe.successThreshold }}
             timeoutSeconds: {{ .Values.saturn.livenessProbe.timeoutSeconds }}
           readinessProbe:
             httpGet:
-              path:  /api/health/
-              port: 8090
+              path:  /actuator/health/readiness
+              port: 8091
             periodSeconds: {{ .Values.saturn.readinessProbe.periodSeconds }}
             successThreshold: {{ .Values.saturn.readinessProbe.successThreshold }}
             timeoutSeconds: {{ .Values.saturn.readinessProbe.timeoutSeconds }}
@@ -222,4 +222,4 @@ spec:
       storageClassName: {{ index .Values "saturn" "persistence" "extra-file-storage" "storageClass" | quote }}
   {{- end }}
 {{- end }}
-{{- end }}
+{{- end }}

local-development/fairspace/local-values.yaml

@@ -25,15 +25,15 @@ fairspace:
     JupyterHub:
       name: "JupyterHub"
       url: http://jupyterhub.local/user/${username}/lab
-      icons-name: jupyter
+      icon-name: jupyter
   metadata-sources:
     internal:
       label: "Metadata"
       icon-name: metadata
     test:
       name: test
       label: "External Metadata"
-      url: http://pluto.local/api/
+      url: http://fairspace.local/api/
       icon-name: "test-icon"
 
 # Specific settings for Saturn subchart

projects/mercury/package.json

@@ -7,13 +7,12 @@
     "dev-be": "concurrently \"yarn localdevelopment\" \"yarn saturn\" \"yarn pluto\"",
     "dev-fe": "yarn build && yarn start",
     "localdevelopment": "cd ../../local-development && docker compose up",
-    "saturn": "wait-on http://localhost:5100/ && wait-on tcp:9432 && cd ../saturn/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew run",
-    "pluto": "wait-on http://localhost:8090/api/health/ && cd ../pluto/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew bootRun --args='--spring.profiles.active=local'",
+    "saturn": "wait-on http://localhost:5100/ && wait-on tcp:9432 && cd ../saturn/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew bootRun",
+    "pluto": "wait-on http://localhost:8091/actuator/health/ && cd ../pluto/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew bootRun --args='--spring.profiles.active=local'",
     "start": "craco start",
     "build": "yarn check-format && craco build",
     "test": "craco test --env=jsdom",
     "test:coverage": "craco test --env=jsdom --coverage --watchAll=false",
-    "eject": "react-scripts eject",
     "lint": "eslint ./src",
     "flow": "flow",
     "format": "prettier --write './**/*.{js,jsx,css,md,json}' --config ./.prettierrc.js",
@@ -32,14 +31,14 @@
     "@testing-library/react-hooks": "^8.0.1",
     "@wojtekmaj/enzyme-adapter-react-17": "^0.8.0",
     "axios": "^1.7.5",
-    "body-parser": "^1.19.0",
+    "body-parser": "^1.20.3",
     "classnames": "^2.2.6",
     "cors": "^2.8.5",
     "date-fns": "^2.29.3",
     "deepmerge": "^4.2.2",
     "escape-string-regexp": "^5.0.0",
     "filesize": "^8.0.7",
-    "http-proxy-middleware": "^2.0.4",
+    "http-proxy-middleware": "^3.0.3",
     "jsonld": "8.2.0",
     "lodash": "^4.17.21",
     "mdi-material-ui": "^7.2.0",
@@ -52,20 +51,21 @@
     "react-dropzone": "^14.2.3",
     "react-is-mounted-hook": "^1.1.2",
     "react-markdown": "^7.1.2",
-    "react-router-dom": "5.3.0",
+    "react-router-dom": "5.3.4",
     "react-scripts": "^5.0.1",
     "react-select": "^5.7.0",
     "react-virtualized": "^9.22.3",
     "react-window": "^1.8.8",
     "text-table": "^0.2.0",
     "typeface-roboto": "^1.1.13",
     "use-deep-compare-effect": "^1.3.0",
-    "webdav": "^4.11.2"
+    "webdav": "^4.11.4"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^5.16.5",
     "@testing-library/react": "^13.4.0",
     "@testing-library/user-event": "^14.4.3",
+    "@babel/plugin-proposal-private-property-in-object": "^7.21.11",
     "concurrently": "^5.0.0",
     "enzyme": "^3.11.0",
     "eslint": "^8.57.0",
@@ -77,11 +77,11 @@
     "eslint-plugin-jsx-a11y": "^6.2.3",
     "eslint-plugin-prettier": "^5.1.3",
     "eslint-plugin-react-hooks": "^4.6.0",
-    "express-session": "^1.17.1",
+    "express-session": "^1.18.1",
     "flow-bin": "^0.117.0",
     "hermes-eslint": "^0.20.0",
     "history": "^5.0.0",
-    "keycloak-connect": "^24.0.1",
+    "keycloak-connect": "^26.0.6",
     "node-fetch": "^2.6.1",
     "nodemon": "^3.1.0",
     "prettier": "^3.2.5",
@@ -95,7 +95,7 @@
     "not op_mini all"
   ],
   "engines": {
-    "node": ">=18.16.0"
+    "node": ">=22.11.0"
   },
   "jest": {
     "moduleNameMapper": {