JDODataStoreExceptions after startup

Current Behavior

I have now seen 3 occasions of the below problem, maybe someone recognizes this.

We're running DT 4.6.2 in docker in ECS with postgres RDS instances as datastore and a volume for the DT /data directory.

Every week updates are installed on the Docker host OS (EC2, Debian 11). This usually triggers an EC2 restart, and thus a docker restart.

The containers come up succesfully and users can browse DT from the UI. Also most API calls work fine, but not all of them.

Example 1: /api/v1/project/lookup

Everything seems to be working, except /api/v1/lookup?name=bla&version=xyz:

2022-11-02 21:06:23,000 ERROR [GlobalExceptionHandler] Uncaught internal server error
javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'alpine.model.Team' AS "DN_TYPE",,"A1"."ID""A1"."ID","A1"."NAME""A1"."NAME" AS "NUCORDER0",,"A1"."UUID","A1"."UUID", FROM  FROM "APIKEYS_TEAMS" "A0" INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE  INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE EXISTS (SELECT 'alpine.model.ApiKey''alpine.model.ApiKey' AS "DN_TYPE", AS "DN_TYPE","A0_SUB"."ID""A0_SUB"."ID" AS "DN_APPID" FROM "APIKEY" "A0_SUB""APIKEY" "A0_SUB" WHERE "A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID""A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"EXISTS (SELECT 'alpine.model.ApiKey''alpine.model.ApiKey' AS "DN_TYPE", AS "DN_TYPE","A0_SUB"."ID""A0_SUB"."ID" AS "DN_APPID" FROM "APIKEY" "A0_SUB""APIKEY" "A0_SUB" WHERE "A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID""A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"
        at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605)
        at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456)
        at org.datanucleus.api.jdo.JDOQuery.execute(JDOQuery.java:276)
        at alpine.persistence.AlpineQueryManager.getApiKey(AlpineQueryManager.java:102)
        at alpine.server.auth.ApiKeyAuthenticationService.authenticate(ApiKeyAuthenticationService.java:67)
...
Caused by: org.postgresql.util.PSQLException: No value specified for parameter 2.
        at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:284)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:340)
        at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413)

Other calls, using the same API Key value, are working fine.

This code is in the Alpine framework and about retrieving an APIKey. However the query contains only 1 parameter:

https://github.com/stevespringett/Alpine/blob/157958bfe7fa5ad95e653667f7ce3282aed23af1/alpine-infra/src/main/java/alpine/persistence/AlpineQueryManager.java#L100-L104

permalink doesn't work it seems, here's the code:

    public ApiKey getApiKey(final String key) {
        final Query query = pm.newQuery(ApiKey.class, "key == :key");
        final List<ApiKey> result = (List<ApiKey>) query.execute(key);
        return Collections.isEmpty(result) ? null : result.get(0);
    }

Which should be translated by datanucleus into 2 parameters in the SQL query seen above. So it's a mystery how parameter 1 can be set, but parameter 2 can be empty.

I spent some time digging around, but couldn't explain this. So decided to take a professional approach: restart docker (so both containers).

This solved the problem.

Example 2: /api/v1/project/

Everything seems to be working, except /api/v1/project/:

curl -X 'GET' \
  'https://dependencytrack-eindhoven.isaac.nl/api/v1/project/yy' \
  -H 'accept: application/json' \
  -H 'X-Api-Key: xx'  
Uncaught internal server error

Exception

2022-11-08 00:00:02,614 [] ERROR [alpine.server.resources.GlobalExceptionHandler] Uncaught internal server error
javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'alpine.model.Team''alpine.model.Team' AS "DN_TYPE","A1"."ID""A1"."ID","A1"."NAME""A1"."NAME" AS "NUCORDER0",,"A1"."UUID","A0"
."PROJECT_ID""A0"."PROJECT_ID" FROM  FROM "PROJECT_ACCESS_TEAMS" "A0" INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE  INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE EXIS
TS (SELECT 'org.dependencytrack.model.Project''org.dependencytrack.model.Project' AS "DN_TYPE" AS "DN_TYPE",,"A0_SUB"."ID" AS "DN_APPID" FROM  FROM "PROJECT" "A0_SUB""PROJECT" "A0_SUB" WHERE "A
0_SUB"."UUID" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"EXISTS (SELECT 'org.dependencytrack.model.Project''org.dependencytrack.model.Project' AS "DN_TYPE" AS "DN_TYPE",,"A0
_SUB"."ID" AS "DN_APPID" FROM  FROM "PROJECT" "A0_SUB""PROJECT" "A0_SUB" WHERE "A0_SUB"."UUID" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"
        at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605)
        at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456)
        at org.datanucleus.api.jdo.JDOQuery.execute(JDOQuery.java:276)
        at alpine.persistence.AbstractAlpineQueryManager.getObjectByUuid(AbstractAlpineQueryManager.java:549)
        at alpine.persistence.AbstractAlpineQueryManager.getObjectByUuid(AbstractAlpineQueryManager.java:563)
        at org.dependencytrack.resources.v1.ProjectResource.getProject(ProjectResource.java:113)

...

Caused by: org.postgresql.util.PSQLException: No value specified for parameter 2.
        at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:284)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:340)

Again this doesn't make sense as there is only 1 paramater uuid, and again parameter 2 is considered empty?

Restarted docker, problem solved.

Example 3: /api/v1/project/lookup (again)

Everything seems to be working, except /api/v1/project/lookup?name=valentijn&version=master:

curl -X 'GET' \
  'https://deptrack/api/v1/project/lookup?name=some%2Fmiddleware+%28java%29&version=master' \
  -H 'accept: application/json' \
  -H 'X-Api-Key: xx'

Uncaught internal server error

Exception

2022-11-10 09:19:35,979 [] ERROR [alpine.server.resources.GlobalExceptionHandler] Uncaught internal server error
javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'org.dependencytrack.model.Tag' AS "DN_TYPE","A1"."ID","A1"."NAME" AS "NUCORDER0","A0"."PROJECT_ID" FROM "PROJECTS_TAGS" "
A0" INNER JOIN "TAG" "A1" ON "A0"."TAG_ID" = "A1"."ID" WHERE EXISTS (SELECT 'org.dependencytrack.model.Project' AS "DN_TYPE","A0_SUB"."ID" AS "DN_APPID" FROM "PROJECT" "A0_SUB" WHERE "A0_SU
B"."NAME" = ? AND "A0_SUB"."VERSION" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"'org.dependencytrack.model.Tag' AS "DN_TYPE","A1"."ID","A1"."NAME" AS "NUCORDER0","A0"."P
ROJECT_ID","A1"."NAME" AS "NUCORDER0" FROM "PROJECTS_TAGS" "A0" INNER JOIN "TAG" "A1" ON "A0"."TAG_ID" = "A1"."ID" WHERE EXISTS (SELECT 'org.dependencytrack.model.Project' AS "DN_TYPE","A0_
SUB"."ID" AS "DN_APPID" FROM "PROJECT" "A0_SUB" WHERE "A0_SUB"."NAME" = ? AND "A0_SUB"."VERSION" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"
        at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605)
        at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456)
        at org.datanucleus.api.jdo.JDOQuery.executeWithMap(JDOQuery.java:331)
        at org.dependencytrack.persistence.ProjectQueryManager.getProject(ProjectQueryManager.java:198)
        at org.dependencytrack.persistence.QueryManager.getProject(QueryManager.java:340)
        at org.dependencytrack.resources.v1.ProjectResource.getProject(ProjectResource.java:145)

...

Caused by: org.postgresql.util.PSQLException: No value specified for parameter 3.
        at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:284)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:340)

Parameter 3 is the version. Which is set and should be present in the query as it's mandatory. If I remove the version from the url, it works. DT says project cannot be found. But I haven't checked if that is the actual query returning nothing, or an early exit because the version is mandatory.

Anyway, I already knew a restart would probably fix it, so I gathered some logs and restarted docker again.

Solution

Anyone has any ideas / suggestions?

I realize this might not be a bug in DT nor in Alpine, but maybe others are seeing the same or have some suggestions.

It is not a resourcing issue as this instance is mostly idle with only 1 nightly job to upload 100 BOMs. And a nightly job that retrieves all projects to load them into backstage.

It seems that once the instance is running OK, the problem stays away and it only occurs after a restart.

I have 11 instances of DT, only 1 instances has the above problem. But it's also the only one under heave read load from backstage indexing.

Valentijn

Dependency-Track Version

4.6.2 / docker / ECS / RDS / PostgreSQL 13.7

Full stacktraces

``` 2022-11-02 21:06:23,000 ERROR [GlobalExceptionHandler] Uncaught internal server error javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'alpine.model.Team' AS "DN_TYPE",,"A1"."ID""A1"."ID","A1"."NAME""A1"."NAME" AS "NUCORDER0",,"A1"."UUID","A1"."UUID", FROM FROM "APIKEYS_TEAMS" "A0" INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE EXISTS (SELECT 'alpine.model.ApiKey''alpine.model.ApiKey' AS "DN_TYPE", AS "DN_TYPE","A0_SUB"."ID""A0_SUB"."ID" AS "DN_APPID" FROM "APIKEY" "A0_SUB""APIKEY" "A0_SUB" WHERE "A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID""A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"EXISTS (SELECT 'alpine.model.ApiKey''alpine.model.ApiKey' AS "DN_TYPE", AS "DN_TYPE","A0_SUB"."ID""A0_SUB"."ID" AS "DN_APPID" FROM "APIKEY" "A0_SUB""APIKEY" "A0_SUB" WHERE "A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID""A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0" at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605) at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456) at org.datanucleus.api.jdo.JDOQuery.execute(JDOQuery.java:276) at alpine.persistence.AlpineQueryManager.getApiKey(AlpineQueryManager.java:102) at alpine.server.auth.ApiKeyAuthenticationService.authenticate(ApiKeyAuthenticationService.java:67) at alpine.server.filters.AuthenticationFilter.filter(AuthenticationFilter.java:68) at org.glassfish.jersey.server.ContainerFilteringStage.apply(ContainerFilteringStage.java:108) at org.glassfish.jersey.server.ContainerFilteringStage.apply(ContainerFilteringStage.java:44) at org.glassfish.jersey.process.internal.Stages.process(Stages.java:173) at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:247) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244) at org.glassfish.jersey.internal.Errors.process(Errors.java:292) at org.glassfish.jersey.internal.Errors.process(Errors.java:274) at org.glassfish.jersey.internal.Errors.process(Errors.java:244) at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265) at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:234) at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:684) at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394) at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:358) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205) at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1419) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:764) at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1665) at alpine.server.filters.ContentSecurityPolicyFilter.doFilter(ContentSecurityPolicyFilter.java:225) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at alpine.server.filters.ClickjackingFilter.doFilter(ClickjackingFilter.java:93) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at alpine.server.filters.WhitelistUrlFilter.doFilter(WhitelistUrlFilter.java:166) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:210) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:527) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:131) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:578) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:223) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1571) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:221) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1383) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:176) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:484) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1544) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:174) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1305) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122) at org.eclipse.jetty.server.Server.handle(Server.java:563) at org.eclipse.jetty.server.HttpChannel.lambda$handle$0(HttpChannel.java:505) at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:762) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:497) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:282) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:314) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:100) at org.eclipse.jetty.io.SelectableChannelEndPoint$1.run(SelectableChannelEndPoint.java:53) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.runTask(AdaptiveExecutionStrategy.java:421) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.consumeTask(AdaptiveExecutionStrategy.java:390) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.tryProduce(AdaptiveExecutionStrategy.java:277) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.lambda$new$0(AdaptiveExecutionStrategy.java:139) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:411) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:933) at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1077) at java.base/java.lang.Thread.run(Unknown Source) Caused by: org.postgresql.util.PSQLException: No value specified for parameter 2. at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:284) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:340) at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413) at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190) at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:134) at com.zaxxer.hikari.pool.ProxyPreparedStatement.executeQuery(ProxyPreparedStatement.java:52) at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.executeQuery(HikariProxyPreparedStatement.java) at org.datanucleus.store.rdbms.SQLController.executeStatementQuery(SQLController.java:548) at org.datanucleus.store.rdbms.query.JDOQLQuery.performExecute(JDOQLQuery.java:717) at org.datanucleus.store.query.Query.executeQuery(Query.java:2004) at org.datanucleus.store.query.Query.executeWithArray(Query.java:1893) at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:433) ... 64 common frames omitted ``` ``` 2022-11-08 00:00:02,614 [] ERROR [alpine.server.resources.GlobalExceptionHandler] Uncaught internal server error javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'alpine.model.Team''alpine.model.Team' AS "DN_TYPE","A1"."ID""A1"."ID","A1"."NAME""A1"."NAME" AS "NUCORDER0",,"A1"."UUID","A0" ."PROJECT_ID""A0"."PROJECT_ID" FROM FROM "PROJECT_ACCESS_TEAMS" "A0" INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE EXIS TS (SELECT 'org.dependencytrack.model.Project''org.dependencytrack.model.Project' AS "DN_TYPE" AS "DN_TYPE",,"A0_SUB"."ID" AS "DN_APPID" FROM FROM "PROJECT" "A0_SUB""PROJECT" "A0_SUB" WHERE "A 0_SUB"."UUID" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"EXISTS (SELECT 'org.dependencytrack.model.Project''org.dependencytrack.model.Project' AS "DN_TYPE" AS "DN_TYPE",,"A0 _SUB"."ID" AS "DN_APPID" FROM FROM "PROJECT" "A0_SUB""PROJECT" "A0_SUB" WHERE "A0_SUB"."UUID" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0" at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605) at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456) at org.datanucleus.api.jdo.JDOQuery.execute(JDOQuery.java:276) at alpine.persistence.AbstractAlpineQueryManager.getObjectByUuid(AbstractAlpineQueryManager.java:549) at alpine.persistence.AbstractAlpineQueryManager.getObjectByUuid(AbstractAlpineQueryManager.java:563) at org.dependencytrack.resources.v1.ProjectResource.getProject(ProjectResource.java:113) at jdk.internal.reflect.GeneratedMethodAccessor232.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.base/java.lang.reflect.Method.invoke(Unknown Source) at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:134) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:177) at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:81) at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81) at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:255) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244) at org.glassfish.jersey.internal.Errors.process(Errors.java:292) at org.glassfish.jersey.internal.Errors.process(Errors.java:274) at org.glassfish.jersey.internal.Errors.process(Errors.java:244) at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265) at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:234) at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:684) at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394) at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:358) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205) at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1419) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:764) at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1665) at alpine.server.filters.ContentSecurityPolicyFilter.doFilter(ContentSecurityPolicyFilter.java:225) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at alpine.server.filters.ClickjackingFilter.doFilter(ClickjackingFilter.java:93) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at alpine.server.filters.WhitelistUrlFilter.doFilter(WhitelistUrlFilter.java:166) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:210) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:527) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:131) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:578) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:223) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1571) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:221) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1383) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:176) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:484) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1544) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:174) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1305) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122) at org.eclipse.jetty.server.Server.handle(Server.java:563) at org.eclipse.jetty.server.HttpChannel.lambda$handle$0(HttpChannel.java:505) at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:762) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:497) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:282) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:314) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:100) at org.eclipse.jetty.io.SelectableChannelEndPoint$1.run(SelectableChannelEndPoint.java:53) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.runTask(AdaptiveExecutionStrategy.java:421) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.consumeTask(AdaptiveExecutionStrategy.java:390) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.tryProduce(AdaptiveExecutionStrategy.java:277) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.lambda$new$0(AdaptiveExecutionStrategy.java:139) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:411) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:933) at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1077) at java.base/java.lang.Thread.run(Unknown Source) Caused by: org.postgresql.util.PSQLException: No value specified for parameter 2. at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:284) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:340) at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413) at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190) at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:134) at com.zaxxer.hikari.pool.ProxyPreparedStatement.executeQuery(ProxyPreparedStatement.java:52) at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.executeQuery(HikariProxyPreparedStatement.java) at org.datanucleus.store.rdbms.SQLController.executeStatementQuery(SQLController.java:548) at org.datanucleus.store.rdbms.query.JDOQLQuery.performExecute(JDOQLQuery.java:717) at org.datanucleus.store.query.Query.executeQuery(Query.java:2004) at org.datanucleus.store.query.Query.executeWithArray(Query.java:1893) at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:433) ... 72 common frames omitted ``` ``` 2022-11-10 09:19:35,979 [] ERROR [alpine.server.resources.GlobalExceptionHandler] Uncaught internal server error javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'org.dependencytrack.model.Tag' AS "DN_TYPE","A1"."ID","A1"."NAME" AS "NUCORDER0","A0"."PROJECT_ID" FROM "PROJECTS_TAGS" " A0" INNER JOIN "TAG" "A1" ON "A0"."TAG_ID" = "A1"."ID" WHERE EXISTS (SELECT 'org.dependencytrack.model.Project' AS "DN_TYPE","A0_SUB"."ID" AS "DN_APPID" FROM "PROJECT" "A0_SUB" WHERE "A0_SU B"."NAME" = ? AND "A0_SUB"."VERSION" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"'org.dependencytrack.model.Tag' AS "DN_TYPE","A1"."ID","A1"."NAME" AS "NUCORDER0","A0"."P ROJECT_ID","A1"."NAME" AS "NUCORDER0" FROM "PROJECTS_TAGS" "A0" INNER JOIN "TAG" "A1" ON "A0"."TAG_ID" = "A1"."ID" WHERE EXISTS (SELECT 'org.dependencytrack.model.Project' AS "DN_TYPE","A0_ SUB"."ID" AS "DN_APPID" FROM "PROJECT" "A0_SUB" WHERE "A0_SUB"."NAME" = ? AND "A0_SUB"."VERSION" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0" at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605) at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456) at org.datanucleus.api.jdo.JDOQuery.executeWithMap(JDOQuery.java:331) at org.dependencytrack.persistence.ProjectQueryManager.getProject(ProjectQueryManager.java:198) at org.dependencytrack.persistence.QueryManager.getProject(QueryManager.java:340) at org.dependencytrack.resources.v1.ProjectResource.getProject(ProjectResource.java:145) at jdk.internal.reflect.GeneratedMethodAccessor134.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.base/java.lang.reflect.Method.invoke(Unknown Source) at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:134) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:177) at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:81) at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81) at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:255) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244) at org.glassfish.jersey.internal.Errors.process(Errors.java:292) at org.glassfish.jersey.internal.Errors.process(Errors.java:274) at org.glassfish.jersey.internal.Errors.process(Errors.java:244) at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265) at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:234) at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:684) at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394) at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:358) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205) at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1419) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:764) at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1665) at alpine.server.filters.ContentSecurityPolicyFilter.doFilter(ContentSecurityPolicyFilter.java:225) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at alpine.server.filters.ClickjackingFilter.doFilter(ClickjackingFilter.java:93) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at alpine.server.filters.WhitelistUrlFilter.doFilter(WhitelistUrlFilter.java:166) at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:210) at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:527) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:131) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:578) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:223) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1571) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:221) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1383) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:176) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:484) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1544) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:174) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1305) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122) at org.eclipse.jetty.server.Server.handle(Server.java:563) at org.eclipse.jetty.server.HttpChannel.lambda$handle$0(HttpChannel.java:505) at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:762) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:497) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:282) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:314) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:100) at org.eclipse.jetty.io.SelectableChannelEndPoint$1.run(SelectableChannelEndPoint.java:53) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.runTask(AdaptiveExecutionStrategy.java:421) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.consumeTask(AdaptiveExecutionStrategy.java:390) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.tryProduce(AdaptiveExecutionStrategy.java:277) at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.lambda$new$0(AdaptiveExecutionStrategy.java:139) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:411) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:933) at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1077) at java.base/java.lang.Thread.run(Unknown Source) Caused by: org.postgresql.util.PSQLException: No value specified for parameter 3. at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:284) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:340) at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413) at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190) at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:134) at com.zaxxer.hikari.pool.ProxyPreparedStatement.executeQuery(ProxyPreparedStatement.java:52) at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.executeQuery(HikariProxyPreparedStatement.java) at org.datanucleus.store.rdbms.SQLController.executeStatementQuery(SQLController.java:548) at org.datanucleus.store.rdbms.query.JDOQLQuery.performExecute(JDOQLQuery.java:717) at org.datanucleus.store.query.Query.executeQuery(Query.java:2004) at org.datanucleus.store.query.Query.executeWithMap(Query.java:1911) at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:437) ... 72 common frames omitted ```

Taking a wild guess here, this really looks like an issue in DataNucleus' query compilation and / or caching.

The fact that the issue persists after it occurred for the first time, but is fixable by a restart strongly suggests that the query caching is playing a role.

Initialization of those caches maybe. It happened now every time we installed Debian updates on the host and restarted the host. Possibly since the upgrade to 4.6.x. I wonder what could cause the initialization of something to fail. The database is remote in RDS and available all the time. Will try to enable DEBUG logging for datanucleus. Looking at the code they are logging parameters etc, so that might give a clue and/or more information to log an issue at datanucleus.

Had another occurrence, this time with another exception:

javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'alpine.model.Team' AS "DN_TYPE",,,,"A1"."NAME""A1"."NAME" AS "NUCORDER0",,"A1"."UUID""A1"."UUID","A0"."APIKEY_ID" FROM  FROM "APIKEYS_TEAMS" "A0" INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE  WHERE EXISTS (SELECT 'alpine.model.ApiKey''alpine.model.ApiKey' AS "DN_TYPE", AS "DN_TYPE","A0_SUB"."ID" AS "DN_APPID" AS "DN_APPID" FROM "APIKEY" "A0_SUB" WHERE "A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID""A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"EXISTS (SELECT 'alpine.model.ApiKey''alpine.model.ApiKey' AS "DN_TYPE", AS "DN_TYPE","A0_SUB"."ID" AS "DN_APPID" AS "DN_APPID" FROM "APIKEY" "A0_SUB" WHERE "A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID""A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"

Which seems to have been reported before in #409 and #422. One of them refers to increasing / decreasing timeouts. Since my issue occurs right after a reboot it's probably not related to session timeouts.

Got this same behaviour on DependencyTrack 4.9.1

The lookup api /api/v1/project/lookup suddenly started returning Uncaught internal server error with statuscode 500.

Simultenously the logs in DT api-server has following error:

javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'org.dependencytrack.model.ProjectProperty' AS "DN_TYPE","A0"."DESCRIPTION","A0"."GROUPNAME" AS "NUCORDER0","A0"."ID","A0"."PROPERTYNAME" AS "NUCORDER1","A0"."PROPERTYTYPE","A0"."PROPERTYVALUE","A0"."PROJECT_ID" FROM "PROJECT_PROPERTY" "A0" WHERE EXISTS (SELECT 'org.dependencytrack.model.Project' AS "DN_TYPE","A0_SUB"."ID" AS "DN_APPID" FROM "PROJECT" "A0_SUB" WHERE "A0_SUB"."NAME" = ? AND "A0_SUB"."VERSION" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0","NUCORDER1"'org.dependencytrack.model.ProjectProperty' AS "DN_TYPE","A0"."DESCRIPTION","A0"."GROUPNAME" AS "NUCORDER0","A0"."ID","A0"."PROPERTYNAME" AS "NUCORDER1","A0"."PROPERTYTYPE","A0"."PROPERTYVALUE","A0"."PROJECT_ID","A0"."PROPERTYNAME" AS "NUCORDER1" FROM "PROJECT_PROPERTY" "A0" WHERE EXISTS (SELECT 'org.dependencytrack.model.Project' AS "DN_TYPE","A0_SUB"."ID" AS "DN_APPID" FROM "PROJECT" "A0_SUB" WHERE "A0_SUB"."NAME" = ? AND "A0_SUB"."VERSION" = ? AND "A0"."PROJECT_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0","NUCORDER1"
    at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605)
    at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456)
    at org.datanucleus.api.jdo.JDOQuery.executeWithMap(JDOQuery.java:331)
    at org.dependencytrack.persistence.ProjectQueryManager.getProject(ProjectQueryManager.java:240)
    at org.dependencytrack.persistence.QueryManager.getProject(QueryManager.java:369)
    at org.dependencytrack.resources.v1.ProjectResource.getProject(ProjectResource.java:146)
    at jdk.internal.reflect.GeneratedMethodAccessor145.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.base/java.lang.reflect.Method.invoke(Unknown Source)
    at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:146)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:189)
    at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:93)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81)
    at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:256)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:244)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)
    at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:235)
    at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:684)
    at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394)
    at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:358)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)
    at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1419)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:764)
    at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1665)
    at alpine.server.filters.ContentSecurityPolicyFilter.doFilter(ContentSecurityPolicyFilter.java:225)
    at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202)
    at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)
    at alpine.server.filters.ClickjackingFilter.doFilter(ClickjackingFilter.java:93)
    at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202)
    at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)
    at alpine.server.filters.WhitelistUrlFilter.doFilter(WhitelistUrlFilter.java:166)
    at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:210)
    at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:527)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:131)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:578)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:223)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1570)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:221)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1385)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:176)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:484)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1543)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:174)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1307)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
    at org.eclipse.jetty.server.Server.handle(Server.java:563)
    at org.eclipse.jetty.server.HttpChannel.lambda$handle$0(HttpChannel.java:505)
    at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:762)
    at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:497)
    at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:282)
    at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:314)
    at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:100)
    at org.eclipse.jetty.io.SelectableChannelEndPoint$1.run(SelectableChannelEndPoint.java:53)
    at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.runTask(AdaptiveExecutionStrategy.java:416)
    at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.consumeTask(AdaptiveExecutionStrategy.java:385)
    at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.tryProduce(AdaptiveExecutionStrategy.java:272)
    at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.lambda$new$0(AdaptiveExecutionStrategy.java:140)
    at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:411)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:936)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1080)
    at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: No value specified for parameter 3.
    at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:284)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:352)
    at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:498)
    at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:415)
    at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190)
    at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:134)
    at com.zaxxer.hikari.pool.ProxyPreparedStatement.executeQuery(ProxyPreparedStatement.java:52)
    at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.executeQuery(HikariProxyPreparedStatement.java)
    at org.datanucleus.store.rdbms.SQLController.executeStatementQuery(SQLController.java:548)
    at org.datanucleus.store.rdbms.query.JDOQLQuery.performExecute(JDOQLQuery.java:717)
    at org.datanucleus.store.query.Query.executeQuery(Query.java:2004)
    at org.datanucleus.store.query.Query.executeWithMap(Query.java:1911)
    at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:437)
    ... 72 common frames omitted

As a workaround, 
I have restarted DT API-Server and things have started working fine again.
Now the lookup api returns back expected results after restarting.

I looks I'm also encountering this issue in 4.10.1

Jenkins using the dependency-Track plugin tries to push a new BOM in the post build action, which fails with a 500.

docker log for the api container reports this:

2024-04-23 13:00:49,324 ERROR [GlobalExceptionHandler] Uncaught internal server error                                                                                                                                                                                                                                       
javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'alpine.model.Team' AS "DN_TYPE","A1"."ID","A1"."NAME" AS "NUCORDER0","A1"."UUID","A0"."APIKEY_ID" FROM "APIKEYS_TEAMS" "A0" INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" = "A1"."ID" WHERE EXISTS (SELECT 'alpine.model.ApiKey' AS "DN_TYPE","A0_SUB"."ID" A
S "DN_APPID" FROM "APIKEY" "A0_SUB" WHERE "A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"'alpine.model.Team' AS "DN_TYPE","A1"."ID","A1"."NAME" AS "NUCORDER0","A1"."UUID","A0"."APIKEY_ID","A1"."NAME" AS "NUCORDER0" FROM "APIKEYS_TEAMS" "A0" INNER JOIN "TEAM" "A1" ON "A0"."TEAM_ID" =
 "A1"."ID" WHERE EXISTS (SELECT 'alpine.model.ApiKey' AS "DN_TYPE","A0_SUB"."ID" AS "DN_APPID" FROM "APIKEY" "A0_SUB" WHERE "A0_SUB"."APIKEY" = ? AND "A0"."APIKEY_ID" = "A0_SUB"."ID") ORDER BY "NUCORDER0"                                                                                                                
        at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605)                                                                                                                                                                                                                       
        at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456)                                                                                                                                                                                                                                              
        at org.datanucleus.api.jdo.JDOQuery.execute(JDOQuery.java:276)                                                                                                                                                                                                                                                      
        at alpine.persistence.AlpineQueryManager.getApiKey(AlpineQueryManager.java:102)                                                                                                                                                                                                                                     
        at alpine.server.auth.ApiKeyAuthenticationService.authenticate(ApiKeyAuthenticationService.java:67)                                                                                                                                                                                                                 
        at alpine.server.filters.AuthenticationFilter.filter(AuthenticationFilter.java:68)                                                                                                                                                                                                                                  
        at org.glassfish.jersey.server.ContainerFilteringStage.apply(ContainerFilteringStage.java:108)                                                                                                                                                                                                                      
        at org.glassfish.jersey.server.ContainerFilteringStage.apply(ContainerFilteringStage.java:44)                                                                                                                                                                                                                       
        at org.glassfish.jersey.process.internal.Stages.process(Stages.java:173)                                                                                                                                                                                                                                            
        at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:248)                                                                                                                                                                                                                                          
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)                                                                                                                                                                                                                                                     
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)                                                                                                                                                                                                                                                     
        at org.glassfish.jersey.internal.Errors.process(Errors.java:292)                                                                                                                                                                                                                                                    
        at org.glassfish.jersey.internal.Errors.process(Errors.java:274)                                                                                                                                                                                                                                                    
        at org.glassfish.jersey.internal.Errors.process(Errors.java:244)                                                                                                                                                                                                                                                    
        at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)                                                                                                                                                                                                                             
        at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:235)                                                                                                                                                                                                                                        
        at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:684)                                                                                                                                                                                                                               
        at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394)                                                                                                                                                                                                                                     
        at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)                                                                                                                                                                                                                                         
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:358)                                                                                                                                                                                                                                 
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311)                                                                                                                                                                                                                                 
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)                                                                                                                                                                                                                                 
        at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1419)                                                                                                                                                                                                                                
        at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:764)                                                                                                                                                                                                                                           
        at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1665)                                                                                                                                                                                                                             
        at alpine.server.filters.ContentSecurityPolicyFilter.doFilter(ContentSecurityPolicyFilter.java:225)                                                                                                                                                                                                                 
        at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202)                                                                                                                                                                                                                                           
        at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)                                                                                                                                                                                                                                
        at alpine.server.filters.ClickjackingFilter.doFilter(ClickjackingFilter.java:93)
        at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202)
        at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)
        at alpine.server.filters.WhitelistUrlFilter.doFilter(WhitelistUrlFilter.java:166)
        at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:210)
        at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)
        at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:527)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:131)
        at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:598)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:223)
        at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1570)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:221)
        at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1384)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:176)
        at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:484)
        at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1543)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:174)
        at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1306)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
        at org.eclipse.jetty.server.Server.handle(Server.java:563)
        at org.eclipse.jetty.server.HttpChannel$RequestDispatchable.dispatch(HttpChannel.java:1598)
        at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:753)
        at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:501)
        at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:287)
        at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:314)
        at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:100)
        at org.eclipse.jetty.io.SelectableChannelEndPoint$1.run(SelectableChannelEndPoint.java:53)
        at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.runTask(AdaptiveExecutionStrategy.java:421)
        at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.consumeTask(AdaptiveExecutionStrategy.java:390)
        at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.tryProduce(AdaptiveExecutionStrategy.java:277)
        at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.run(AdaptiveExecutionStrategy.java:199)
        at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:411)
        at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:969)
        at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.doRunJob(QueuedThreadPool.java:1194)
        at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1149)
        at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: No value specified for parameter 2.
        at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:284)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:352)
        at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:498)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:415)
        at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190)
        at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:134)
        at com.zaxxer.hikari.pool.ProxyPreparedStatement.executeQuery(ProxyPreparedStatement.java:52)
        at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.executeQuery(HikariProxyPreparedStatement.java)
        at org.datanucleus.store.rdbms.SQLController.executeStatementQuery(SQLController.java:548)
        at org.datanucleus.store.rdbms.query.JDOQLQuery.performExecute(JDOQLQuery.java:717)
        at org.datanucleus.store.query.Query.executeQuery(Query.java:2004)
        at org.datanucleus.store.query.Query.executeWithArray(Query.java:1893)
        at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:433)
        ... 65 common frames omitted

Docker was recently updated from 5:26.0.2-1~debian.11~bullseye to 5:26.1.0-1~debian.11~bullseye.

After running docker compose down && docker compose up -d dependency-track accepts new BOMs once again.

Solved on our side by removing the index directory and restarting the app

No idea of the root cause tho. The server just broke by itself during the weekend

We're getting something similar in the error logs when a user tries to expand a project which contains child projects:

2024-09-11 09:19:36,768 ERROR [GlobalExceptionHandler] Uncaught internal server error
javax.jdo.JDODataStoreException: Iteration request failed : SELECT 'org.dependencytrack.model.Tag''org.dependencytrack.model.Tag' AS "DN_TYPE", AS "DN_TYPE","A1"."ID","A1"."NAME" AS "NUCORDER0","A0"."PROJECT_ID","A1"."NAME" AS "NUCORDER0" FROM "PROJECTS_TAGS" "A0" INNER JOIN "TAG" "A1" ON "A0"."TAG_ID" = "A1"."ID" WHERE EXISTS (SELECT 'org.dependencytrack.model.Project' AS "DN_TYPE","A0_SUB"."ID" AS "DN_APPID" FROM "PROJECT" "A0_SUB" WHERE "A0_SUB"."UUID" = ? AND "A0"."PROJECT_ID" =                         "A0_SUB"."ID") ORDER BY "NUCORDER0"
        at org.datanucleus.api.jdo.JDOAdapter.getJDOExceptionForNucleusException(JDOAdapter.java:605)
        at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:456)
        at org.datanucleus.api.jdo.JDOQuery.execute(JDOQuery.java:276)
        at alpine.persistence.AbstractAlpineQueryManager.getObjectByUuid(AbstractAlpineQueryManager.java:549)
        at alpine.persistence.AbstractAlpineQueryManager.getObjectByUuid(AbstractAlpineQueryManager.java:563)
        at org.dependencytrack.resources.v1.FindingResource.getFindingsByProject(FindingResource.java:107)
        at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(Unknown Source)
        at java.base/java.lang.reflect.Method.invoke(Unknown Source)
        at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52)
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:146)
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:189)
        at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176)
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:93)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81)
        at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:256)
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:244)
        at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)
        at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:235)
        at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:684)
        at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394)
        at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:358)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)
        at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1419)
        at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:764)
        at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1665)
        at alpine.server.filters.ContentSecurityPolicyFilter.doFilter(ContentSecurityPolicyFilter.java:225)
        at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202)
        at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)
        at alpine.server.filters.ClickjackingFilter.doFilter(ClickjackingFilter.java:93)
        at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202)
        at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)
        at alpine.server.filters.WhitelistUrlFilter.doFilter(WhitelistUrlFilter.java:166)
        at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:210)
        at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635)
        at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:527)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:131)
        at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:598)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:223)
        at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1570)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:221)
        at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1384)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:176)
        at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:484)
        at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1543)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:174)
        at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1306)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
        at org.eclipse.jetty.server.Server.handle(Server.java:563)
        at org.eclipse.jetty.server.HttpChannel$RequestDispatchable.dispatch(HttpChannel.java:1598)
        at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:753)
        at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:501)
        at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:287)
        at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:314)
        at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:100)
        at org.eclipse.jetty.io.SelectableChannelEndPoint$1.run(SelectableChannelEndPoint.java:53)
        at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.runTask(AdaptiveExecutionStrategy.java:421)
        at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.consumeTask(AdaptiveExecutionStrategy.java:390)
        at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.tryProduce(AdaptiveExecutionStrategy.java:277)
        at org.eclipse.jetty.util.thread.strategy.AdaptiveExecutionStrategy.run(AdaptiveExecutionStrategy.java:199)
        at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:411)
        at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:969)
        at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.doRunJob(QueuedThreadPool.java:1194)
        at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1149)
        at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: ERROR: syntax error at or near "AS"
  Position: 85
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2725)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2412)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:371)
        at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:502)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:419)
        at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:194)
        at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:137)
        at com.zaxxer.hikari.pool.ProxyPreparedStatement.executeQuery(ProxyPreparedStatement.java:52)
        at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.executeQuery(HikariProxyPreparedStatement.java)
        at org.datanucleus.store.rdbms.SQLController.executeStatementQuery(SQLController.java:584)
        at org.datanucleus.store.rdbms.query.JDOQLQuery.performExecute(JDOQLQuery.java:717)
        at org.datanucleus.store.query.Query.executeQuery(Query.java:2004)
        at org.datanucleus.store.query.Query.executeWithArray(Query.java:1893)
        at org.datanucleus.api.jdo.JDOQuery.executeInternal(JDOQuery.java:433)
        ... 72 common frames omitted

Deleting the k8s pod helps, but the issue re-appears randomly

I think the root cause is the same as for https://github.com/DependencyTrack/dependency-track/issues/2061 (underlying issue here: https://github.com/datanucleus/datanucleus-rdbms/issues/491).

So this should be fixed in v4.12.

Closing this as fixed for v4.12. The example error logs shared here all show the same symptom of partial or incorrectly assembled SQL queries, which matches the behavior described in https://github.com/datanucleus/datanucleus-rdbms/issues/491.

Please open a new issue if these errors persist post v4.12 upgrade.

DependencyTrack / dependency-track