SonarQube empty after upgrade from 8.9 to 9.9

I have a swarm stack with a SonarQube 8.9-community service and a postgres 16.3 service. I want to upgrade my sonarQube to 9.9-community. But, when i try, it systematically act as it was a fresh install, recreating all the database and deleting all the plugins. As a result, i lose all my projets and need to rollback and restore my last backup…

My docker-compose is as following (the only thing i change is the version of sonarqube):

version: "3.6"

services:
  sonarqube:
    image: sonarqube:8.9-community
    ports:
      - "9001:9000"
    networks:
      - sonar
    environment:
      - SONARQUBE_JDBC_URL=jdbc:postgresql://db:5432/sonar
      - SONARQUBE_JDBC_USERNAME=sonar
      - SONARQUBE_JDBC_PASSWORD=test
    security_opt:
      - "seccomp=/seccomp.js"
    volumes:
      - /sonar/sonar_qube/conf:/opt/sonarqube/conf
      - /sonar/sonar_qube/logs:/opt/sonarqube/logs
      - /sonar/sonar_qube/data:/opt/sonarqube/data
      - /sonar/sonar_qube/extensions:/opt/sonarqube/extensions
      - /sonar/sonar_qube/bundled-plugins:/opt/sonarqube/lib/bundled-plugins
    deploy:
      resources:
        limits:
          memory: 5G
        reservations:
          memory: 5G
      placement:
        constraints:
          - node.role==worker
  db:
    image: postgres:16.3
    networks:
      - sonarnet
    environment:
      - POSTGRES_USER=sonar
      - POSTGRES_PASSWORD=test
    volumes:
      - /sonar/postgresql:/var/lib/postgresql
      - /sonar/postgresql_data:/var/lib/postgresql/data
    deploy:
      resources:
        limits:
          memory: 1G
        reservations:
          memory: 1G
      placement:
        constraints:
          - node.role==worker
networks:
  sonar

The only thing i could think of to fix it was to perform an intermediate update. The upgrade works fine with version 9.6 and 9.8 but after that, it’s all the same. The logs explicitly state that the migration is triggered automatically because it consider it as a fresh install (meaning dropping and recreating the database):

2024.06.13 15:05:41 INFO  app[][o.s.a.AppFileSystem] Cleaning or creating temp directory /opt/sonarqube/temp
2024.06.13 15:05:41 INFO  app[][o.s.a.es.EsSettings] Elasticsearch listening on [HTTP: 127.0.0.1:9001, TCP: 127.0.0.1:40425]
2024.06.13 15:05:41 INFO  app[][o.s.a.ProcessLauncherImpl] Launch process[ELASTICSEARCH] from [/opt/sonarqube/elasticsearch]: /opt/sonarqube/elasticsearch/bin/elasticsearch
2024.06.13 15:05:41 INFO  app[][o.s.a.SchedulerImpl] Waiting for Elasticsearch to be up and running
2024.06.13 15:05:43 INFO  es[][o.e.n.Node] version[7.17.15], pid[26], build[default/tar/0b8ecfb4378335f4689c4223d1f1115f16bef3ba/2023-11-10T22:03:46.987399016Z], OS[Linux/5.14.0-284.11.1.el9_2.x86_64/amd64], JVM[Eclipse Adoptium/OpenJDK 64-Bit Server VM/17.0.11/17.0.11+9]
2024.06.13 15:05:43 INFO  es[][o.e.n.Node] JVM home [/opt/java/openjdk]
2024.06.13 15:05:43 INFO  es[][o.e.n.Node] JVM arguments [-XX:+UseG1GC, -Djava.io.tmpdir=/opt/sonarqube/temp, -XX:ErrorFile=/opt/sonarqube/logs/es_hs_err_pid%p.log, -Des.networkaddress.cache.ttl=60, -Des.networkaddress.cache.negative.ttl=10, -XX:+AlwaysPreTouch, -Xss1m, -Djava.awt.headless=true, -Dfile.encoding=UTF-8, -Djna.nosys=true, -Djna.tmpdir=/opt/sonarqube/temp, -XX:-OmitStackTraceInFastThrow, -Dio.netty.noUnsafe=true, -Dio.netty.noKeySetOptimization=true, -Dio.netty.recycler.maxCapacityPerThread=0, -Dio.netty.allocator.numDirectArenas=0, -Dlog4j.shutdownHookEnabled=false, -Dlog4j2.disable.jmx=true, -Dlog4j2.formatMsgNoLookups=true, -Djava.locale.providers=COMPAT, -Dcom.redhat.fips=false, -Xmx1024m, -Xms1024m, -XX:+HeapDumpOnOutOfMemoryError, -Des.path.home=/opt/sonarqube/elasticsearch, -Des.path.conf=/opt/sonarqube/temp/conf/es, -Des.distribution.flavor=default, -Des.distribution.type=tar, -Des.bundled_jdk=false]
2024.06.13 15:05:43 INFO  es[][o.e.p.PluginsService] loaded module [analysis-common]
2024.06.13 15:05:43 INFO  es[][o.e.p.PluginsService] loaded module [lang-painless]
2024.06.13 15:05:43 INFO  es[][o.e.p.PluginsService] loaded module [parent-join]
2024.06.13 15:05:43 INFO  es[][o.e.p.PluginsService] loaded module [reindex]
2024.06.13 15:05:43 INFO  es[][o.e.p.PluginsService] loaded module [transport-netty4]
2024.06.13 15:05:43 INFO  es[][o.e.p.PluginsService] no plugins loaded
2024.06.13 15:05:43 INFO  es[][o.e.e.NodeEnvironment] using [1] data paths, mounts [[/opt/sonarqube/data (SFL052101:/data.di.dockerdivers/sonar-test/sonar/sonar_qube/data)]], net usable_space [181.4gb], net total_space [282.9gb], types [nfs]
2024.06.13 15:05:43 INFO  es[][o.e.e.NodeEnvironment] heap size [1gb], compressed ordinary object pointers [true]
2024.06.13 15:05:43 INFO  es[][o.e.n.Node] node name [sonarqube], node ID [I7VCwqA6QReMUphdC9Pgnw], cluster name [sonarqube], roles [data_frozen, master, remote_cluster_client, data, data_content, data_hot, data_warm, data_cold, ingest]
2024.06.13 15:05:46 INFO  es[][o.e.t.NettyAllocator] creating NettyAllocator with the following configs: [name=unpooled, suggested_max_allocation_size=256kb, factors={es.unsafe.use_unpooled_allocator=null, g1gc_enabled=true, g1gc_region_size=1mb, heap_size=1gb}]
2024.06.13 15:05:46 INFO  es[][o.e.i.r.RecoverySettings] using rate limit [40mb] with [default=40mb, read=0b, write=0b, max=0b]
2024.06.13 15:05:46 INFO  es[][o.e.d.DiscoveryModule] using discovery type [zen] and seed hosts providers [settings]
2024.06.13 15:05:46 INFO  es[][o.e.g.DanglingIndicesState] gateway.auto_import_dangling_indices is disabled, dangling indices will not be automatically detected or imported and must be managed manually
2024.06.13 15:05:46 INFO  es[][o.e.n.Node] initialized
2024.06.13 15:05:46 INFO  es[][o.e.n.Node] starting ...
2024.06.13 15:05:46 INFO  es[][o.e.t.TransportService] publish_address {127.0.0.1:40425}, bound_addresses {127.0.0.1:40425}
2024.06.13 15:05:47 INFO  es[][o.e.c.c.Coordinator] cluster UUID [vdJAXekLTfu_RwLqOF-2Fg]
2024.06.13 15:05:47 INFO  es[][o.e.c.s.MasterService] elected-as-master ([1] nodes joined)[{sonarqube}{I7VCwqA6QReMUphdC9Pgnw}{e9zQPE-vSfK6VUnuB1ffhQ}{127.0.0.1}{127.0.0.1:40425}{cdfhimrsw} elect leader, _BECOME_MASTER_TASK_, _FINISH_ELECTION_], term: 20, version: 401, delta: master node changed {previous [], current [{sonarqube}{I7VCwqA6QReMUphdC9Pgnw}{e9zQPE-vSfK6VUnuB1ffhQ}{127.0.0.1}{127.0.0.1:40425}{cdfhimrsw}]}
2024.06.13 15:05:47 INFO  es[][o.e.c.s.ClusterApplierService] master node changed {previous [], current [{sonarqube}{I7VCwqA6QReMUphdC9Pgnw}{e9zQPE-vSfK6VUnuB1ffhQ}{127.0.0.1}{127.0.0.1:40425}{cdfhimrsw}]}, term: 20, version: 401, reason: Publication{term=20, version=401}
2024.06.13 15:05:47 INFO  es[][o.e.h.AbstractHttpServerTransport] publish_address {127.0.0.1:9001}, bound_addresses {127.0.0.1:9001}
2024.06.13 15:05:47 INFO  es[][o.e.n.Node] started
2024.06.13 15:05:47 INFO  es[][o.e.g.GatewayService] recovered [7] indices into cluster_state
2024.06.13 15:05:49 INFO  es[][o.e.c.r.a.AllocationService] Cluster health status changed from [RED] to [GREEN] (reason: [shards started [[projectmeasures][3], [projectmeasures][2], [metadatas][0]]]).
2024.06.13 15:05:50 INFO  app[][o.s.a.SchedulerImpl] Process[es] is up
2024.06.13 15:05:50 INFO  app[][o.s.a.ProcessLauncherImpl] Launch process[WEB_SERVER] from [/opt/sonarqube]: /opt/java/openjdk/bin/java -Djava.awt.headless=true -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/opt/sonarqube/temp -XX:-OmitStackTraceInFastThrow --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED --add-exports=java.base/jdk.internal.ref=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.management/sun.management=ALL-UNNAMED --add-opens=jdk.management/com.sun.management.internal=ALL-UNNAMED -Dcom.redhat.fips=false -Xmx512m -Xms128m -XX:+HeapDumpOnOutOfMemoryError -Dhttp.nonProxyHosts=localhost|127.*|[::1] -cp ./lib/sonar-application-9.9.5.90363.jar:/opt/sonarqube/lib/jdbc/h2/h2-2.1.214.jar org.sonar.server.app.WebServer /opt/sonarqube/temp/sq-process6380220738101035128properties
WARNING: A terminally deprecated method in java.lang.System has been called
WARNING: System::setSecurityManager has been called by org.sonar.process.PluginSecurityManager (file:/opt/sonarqube/lib/sonar-application-9.9.5.90363.jar)
WARNING: Please consider reporting this to the maintainers of org.sonar.process.PluginSecurityManager
WARNING: System::setSecurityManager will be removed in a future release
2024.06.13 15:05:50 INFO  web[][o.s.p.ProcessEntryPoint] Starting Web Server
2024.06.13 15:05:51 INFO  web[][o.s.s.p.LogServerVersion] SonarQube Server / 9.9.5.90363 / dfc7d8d716ea13cce42ab9d806d74568f3f4693f
2024.06.13 15:05:51 INFO  web[][o.s.s.p.d.EmbeddedDatabase] Starting embedded database on port 9092 with url jdbc:h2:tcp://127.0.0.1:9092/sonar;NON_KEYWORDS=VALUE
2024.06.13 15:05:51 INFO  web[][o.s.s.p.d.EmbeddedDatabase] Embedded database started. Data stored in: /opt/sonarqube/data
2024.06.13 15:05:51 INFO  web[][o.sonar.db.Database] Create JDBC data source for jdbc:h2:tcp://127.0.0.1:9092/sonar;NON_KEYWORDS=VALUE
2024.06.13 15:05:51 INFO  web[][c.z.h.HikariDataSource] HikariPool-1 - Starting...
2024.06.13 15:05:51 INFO  web[][c.z.h.p.HikariPool] HikariPool-1 - Added connection conn2: url=jdbc:h2:tcp://127.0.0.1:9092/sonar user=
2024.06.13 15:05:51 INFO  web[][c.z.h.HikariDataSource] HikariPool-1 - Start completed.
2024.06.13 15:05:51 WARN  web[][o.s.db.dialect.H2] H2 database should be used for evaluation purpose only.
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerFileSystemImpl] SonarQube home: /opt/sonarqube
2024.06.13 15:05:52 INFO  web[][o.s.s.u.SystemPasscodeImpl] System authentication by passcode is disabled
2024.06.13 15:05:52 INFO  web[][o.s.s.p.d.m.h.MigrationHistoryTableImpl] Creating table schema_migrations
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy C# Code Quality and Security / 8.51.0.59060 / e14c642f118958f22fd08841dc42f9aae480366a
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Configuration detection fot Code Quality and Security / 1.2.0.267 / 4f37ba9ffb37a96d5883e52ad392ed32c5c6eaab
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Flex Code Quality and Security / 2.8.0.3166 / 01f66bdddc678966c81a9064ed139156a6a89c97
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Go Code Quality and Security / 1.11.0.3905 / e1f28bc000e04ca01881e84218d01d464a17a36f
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy HTML Code Quality and Security / 3.7.1.3306 / d720acc6860c6d8b69ec4d17570a398a1e216da1
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy IaC Code Quality and Security / 1.11.0.2847 / 6892bd3a7320b3c110717acfdb18c4c7451069fd
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy JaCoCo / 1.3.0.1538 / 74a7798c7cea687c72ed9df40c93eb7ea2a58c49
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Java Code Quality and Security / 7.16.0.30901 / 4b1436558dfd5fc00c8d9aae8bb0364ba122c73e
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy JavaScript/TypeScript/CSS Code Quality and Security / 9.13.0.20537 / 68ff7657415044b86033814795ed95fc1f1558f1
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Kotlin Code Quality and Security / 2.12.0.1956 / a6df1ae252bd62d63f8673c28f87ad14258a7904
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy PHP Code Quality and Security / 3.27.1.9352 / 3ddc5a03e1a7e3729d41e7c1a30a37d5715958c7
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Python Code Quality and Security / 3.24.1.11916 / cc8f4fa745eb33d31c3869bdfdfd45514e67c1fe
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Ruby Code Quality and Security / 1.11.0.3905 / e1f28bc000e04ca01881e84218d01d464a17a36f
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Scala Code Quality and Security / 1.11.0.3905 / e1f28bc000e04ca01881e84218d01d464a17a36f
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy ShellCheck Analyzer / 2.4.0 / null
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy Text Code Quality and Security / 2.0.2.1090 / 7eb026363b98f5f98b43c603772b5177869c2c6a
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy VB.NET Code Quality and Security / 8.51.0.59060 / e14c642f118958f22fd08841dc42f9aae480366a
2024.06.13 15:05:52 INFO  web[][o.s.s.p.ServerPluginManager] Deploy XML Code Quality and Security / 2.7.0.3820 / 656bccc1910d50c8984536bd2dfd917066b858e6
2024.06.13 15:05:54 INFO  web[][o.s.s.e.EsClientProvider] Connected to local Elasticsearch: [http://localhost:9001]
2024.06.13 15:05:54 WARN  web[][o.s.a.s.w.WebService$Action] Description is not set on action api/monitoring/metrics
2024.06.13 15:05:54 WARN  web[][o.s.a.s.w.WebService$Action] Since is not set on action api/monitoring/metrics
2024.06.13 15:05:54 WARN  web[][o.s.a.s.w.WebService$Action] The response example is not set on action api/monitoring/metrics
2024.06.13 15:05:54 WARN  web[][o.s.a.s.w.WebService$Action] The response example is not set on action api/system/liveness
2024.06.13 15:05:54 INFO  web[][o.s.s.p.d.m.AutoDbMigration] Automatically perform DB migration on fresh install

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