Stream: ibm
Topic: FHIR DB issues
Purush Das (Aug 07 2020 at 19:30):
Hi,
Installed v4.3.3. and using single embedded Derby database.
I did a curl $healthcheck and got error response:
{"resourceType":"OperationOutcome","id":"7f-0-0-1-97f933f8-17fa-4e4a-aa28-d7539abd73a0","issue":[{"severity":"fatal","code":"exception","details":{"text":"The FHIR Server web application cannot process requests because it did not initialize correctly"}}]
Seeing following errors in the logs after starting fhir server.
any help would be appreciated..
[8/7/20 14:52:34:905 EDT] 00000032 com.ibm.fhir.persistence.jdbc.util.DerbyBootstrapper E Encountered an exception while bootstrapping the FHIR database
com.ibm.fhir.database.utils.api.ConnectionException: java.sql.SQLNonTransientConnectionException: No current connection.
at com.ibm.fhir.database.utils.derby.DerbyTranslator.translate(DerbyTranslator.java:88)
at com.ibm.fhir.database.utils.common.JdbcTarget.runStatement(JdbcTarget.java:41)
at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:225)
at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.createForeignKeyConstraint(CommonDatabaseAdapter.java:355)
at com.ibm.fhir.database.utils.derby.DerbyAdapter.createForeignKeyConstraint(DerbyAdapter.java:277)
at com.ibm.fhir.database.utils.model.ForeignKeyConstraint.apply(ForeignKeyConstraint.java:112)
at com.ibm.fhir.database.utils.model.Table.apply(Table.java:126)
at com.ibm.fhir.database.utils.model.Table.apply(Table.java:145)
at com.ibm.fhir.database.utils.model.BaseObject.applyVersion(BaseObject.java:262)
at com.ibm.fhir.database.utils.model.ObjectGroup.applyVersion(ObjectGroup.java:67)
at com.ibm.fhir.database.utils.model.PhysicalDataModel.applyWithHistory(PhysicalDataModel.java:133)
at com.ibm.fhir.persistence.jdbc.util.DerbyBootstrapper.bootstrap(DerbyBootstrapper.java:133)
at com.ibm.fhir.persistence.jdbc.util.DerbyBootstrapper.bootstrapDb(DerbyBootstrapper.java:81)
at com.ibm.fhir.server.listener.FHIRServletContextListener.bootstrapFhirDb(FHIRServletContextListener.java:282)
at com.ibm.fhir.server.listener.FHIRServletContextListener.bootstrapDerbyDatabases(FHIRServletContextListener.java:216)
at com.ibm.fhir.server.listener.FHIRServletContextListener.contextInitialized(FHIRServletContextListener.java:177)
at com.ibm.ws.webcontainer.webapp.WebApp.notifyServletContextCreated(WebApp.java:2433)
at com.ibm.ws.webcontainer31.osgi.webapp.WebApp31.notifyServletContextCreated(WebApp31.java:514)
at com.ibm.ws.webcontainer.webapp.WebApp.initialize(WebApp.java:1037)
at com.ibm.ws.webcontainer.webapp.WebApp.initialize(WebApp.java:6663)
at com.ibm.ws.webcontainer.osgi.DynamicVirtualHost.startWebApp(DynamicVirtualHost.java:467)
at com.ibm.ws.webcontainer.osgi.DynamicVirtualHost.startWebApplication(DynamicVirtualHost.java:462)
at com.ibm.ws.webcontainer.osgi.WebContainer.startWebApplication(WebContainer.java:1175)
at com.ibm.ws.webcontainer.osgi.WebContainer.startModule(WebContainer.java:967)
at com.ibm.ws.app.manager.module.internal.ModuleHandlerBase.deployModule(ModuleHandlerBase.java:99)
at com.ibm.ws.app.manager.module.internal.DeployedModuleInfoImpl.installModule(DeployedModuleInfoImpl.java:49)
at com.ibm.ws.app.manager.module.internal.SimpleDeployedAppInfoBase.deployModules(SimpleDeployedAppInfoBase.java:597)
at com.ibm.ws.app.manager.module.internal.SimpleDeployedAppInfoBase.installApp(SimpleDeployedAppInfoBase.java:511)
at com.ibm.ws.app.manager.module.internal.DeployedAppInfoBase.deployApp(DeployedAppInfoBase.java:347)
at com.ibm.ws.app.manager.war.internal.WARApplicationHandlerImpl.install(WARApplicationHandlerImpl.java:65)
at com.ibm.ws.app.manager.internal.statemachine.StartAction.execute(StartAction.java:144)
at com.ibm.ws.app.manager.internal.statemachine.ApplicationStateMachineImpl.enterState(ApplicationStateMachineImpl.java:1315)
at com.ibm.ws.app.manager.internal.statemachine.ApplicationStateMachineImpl.run(ApplicationStateMachineImpl.java:897)
at com.ibm.ws.threading.internal.ExecutorServiceImpl$RunnableWrapper.run(ExecutorServiceImpl.java:239)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.sql.SQLNonTransientConnectionException: No current connection.
at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.Util.noCurrentConnection(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection.checkIfClosed(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection.createStatement(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection.createStatement(Unknown Source)
at org.apache.derby.iapi.jdbc.BrokeredConnection.createStatement(Unknown Source)
at com.ibm.ws.rsadapter.jdbc.WSJdbcConnection.createStatement(WSJdbcConnection.java:1075)
at com.ibm.ws.rsadapter.jdbc.WSJdbcConnection.createStatement(WSJdbcConnection.java:1058)
at com.ibm.fhir.database.utils.common.JdbcTarget.runStatement(JdbcTarget.java:37)
Lee Surprenant (Aug 07 2020 at 19:32):
thanks for the report purush, did you do anything with the config or is this just running the official container image (single-node embedded derby is the default)?
Purush Das (Aug 07 2020 at 19:34):
Yes. using default.
Paul Bastide (Aug 07 2020 at 19:35):
We've seen issues like this in our build pipeline when there is a disk performance issue. Is this on a local machine in this case?
Purush Das (Aug 07 2020 at 19:36):
ubuntu-16-04-lts
Purush Das (Aug 07 2020 at 19:40):
btw - Not a workstation. Installed on ubuntu 16-04-lts server
Lee Surprenant (Aug 07 2020 at 19:40):
using the installer or using the docker image?
Lee Surprenant (Aug 07 2020 at 19:41):
assuming the installer, can you grab the messages.log for us from
[yourinstalldir]/wlp/usr/servers/fhir-server/logs?
Lee Surprenant (Aug 07 2020 at 19:42):
mostly, we'll be interested in the timings on the derby bootstrapping
Lee Surprenant (Aug 07 2020 at 19:44):
a healthy startup would look something like this:
[8/7/20 19:39:23:758 UTC] 00000030 com.ibm.fhir.persistence.jdbc.util.DerbyBootstrapper I Performing derby db bootstrapping for tenant-id 'default', datastore-id 'default'.
[8/7/20 19:39:24:983 UTC] 00000030 com.ibm.ws.rsadapter.impl.DatabaseHelper I DSRA8203I: Database product name : Apache Derby
[8/7/20 19:39:24:985 UTC] 00000030 com.ibm.ws.rsadapter.impl.DatabaseHelper I DSRA8204I: Database product version : 10.14.2.0 - (1828579)
[8/7/20 19:39:24:986 UTC] 00000030 com.ibm.ws.rsadapter.impl.DatabaseHelper I DSRA8205I: JDBC driver name : Apache Derby Embedded JDBC Driver
[8/7/20 19:39:24:986 UTC] 00000030 com.ibm.ws.rsadapter.impl.DatabaseHelper I DSRA8206I: JDBC driver version : 10.14.2.0 - (1828579)
[8/7/20 19:39:25:168 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyServerPropertiesMgr I Database Property [derby.language.sequence.preallocator] desired value [10000] and is currently [null]
[8/7/20 19:39:25:183 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyServerPropertiesMgr I Database Property [derby.language.sequence.preallocator] desired value [10000] and is now [10000]
[8/7/20 19:39:25:466 UTC] 00000030 com.ibm.fhir.database.utils.model.DatabaseObject I Applying change [v1]: TABLESPACE:FHIR_TS:1
[8/7/20 19:39:25:632 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyAdapter W [ONCE] Derby does not support CREATE VARIABLE for: SV_TENANT_ID
[8/7/20 19:39:25:635 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyAdapter W [ONCE] Create procedure not supported in Derby
[8/7/20 19:39:25:653 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyAdapter I Recreating sequence 'APP.FHIR_REF_SEQUENCE' START WITH 20000
[8/7/20 19:39:25:660 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyAdapter W [ONCE] Derby does not support multi-tenancy on: [PARAMETER_NAMES]
[8/7/20 19:39:25:686 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyAdapter W [ONCE] Derby does not support CREATE PERMISSION for: PARAMETER_NAMES_TENANT
[8/7/20 19:39:25:687 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyAdapter W [ONCE] Derby does not support ROW ACCESS CONTROL for table: PARAMETER_NAMES
[8/7/20 19:39:26:148 UTC] 00000030 com.ibm.fhir.database.utils.derby.DerbyAdapter W [ONCE] Not supported in Derby: ALTER TABLE APP.APPOINTMENT_STR_VALUES ALTER COLUMN ROW_ID SET CACHE 1000
Purush Das (Aug 07 2020 at 19:51):
it's installer. Here's the message.log file. messages.log
Lee Surprenant (Aug 07 2020 at 20:06):
thanks purush, we'll have a look. did you happen to try multiple times or just this once?
Lee Surprenant (Aug 07 2020 at 20:07):
if you want, you could retry and let us know if it happens again
Purush Das (Aug 07 2020 at 20:07):
I tried stopping and starting couple of times.
Thanks
Lee Surprenant (Aug 07 2020 at 20:10):
one of our ideas is to move this derby bootstrapping out of server startup...its there as a convenience so you can just "docker run" without worrying about it, but it looks like maybe the bootstrapping is taking longer on your system than ours and leading to a transaction timeout. (just based on first error in the logs)
Lee Surprenant (Aug 07 2020 at 20:11):
if you're willing/able to help us debug it further, I can ask you to bump that transaction timeout in your config and see if it helps
Lee Surprenant (Aug 07 2020 at 20:37):
we'd also be curious what kind of the specs for your server. we recommend having 4GB of RAM available to run the FHIR Server (though you can get it smaller if you know how)
Purush Das (Aug 07 2020 at 20:40):
I can try docker. Could you please provide docker image download link?
Lee Surprenant (Aug 07 2020 at 20:41):
docker run -p 9443:9443 ibmcom/ibm-fhir-server:4.3.3
Lee Surprenant (Aug 07 2020 at 20:42):
see https://hub.docker.com/r/ibmcom/ibm-fhir-server for details
Purush Das (Aug 07 2020 at 21:06):
Hi Lee,
I tried docker and throwing similar error: Encountered an exception while bootstrapping the FHIR database
[ERROR ] DSRA0304E: XAException occurred. XAException contents and details are: .
[ERROR ] DSRA0302E: XAException occurred. Error code is: XA_RBROLLBACK (100). Exception is: null
[ERROR ] Encountered an exception while bootstrapping the FHIR database
java.sql.SQLNonTransientConnectionException: No current connection.
[ERROR ] transaction rollback failed
No Global Transaction exists to commit.
[ERROR ] Encountered an exception while initializing the servlet context.
javax.transaction.RollbackException
[ERROR ] SRVE0283E: Exception caught while initializing context: java.lang.RuntimeException: Encountered an exception while initializing the servlet context.
at com.ibm.fhir.server.listener.FHIRServletContextListener.contextInitialized(FHIRServletContextListener.java:195)
at com.ibm.ws.webcontainer.webapp.WebApp.notifyServletContextCreated(WebApp.java:2433)
at [internal classes]
Caused by: javax.transaction.RollbackException
at com.ibm.tx.jta.impl.TransactionImpl.stage3CommitProcessing(TransactionImpl.java:978)
at [internal classes]
at com.ibm.fhir.server.listener.FHIRServletContextListener.bootstrapFhirDb(FHIRServletContextListener.java:286)
at com.ibm.fhir.server.listener.FHIRServletContextListener.bootstrapDerbyDatabases(FHIRServletContextListener.java:216)
at com.ibm.fhir.server.listener.FHIRServletContextListener.contextInitialized(FHIRServletContextListener.java:177)
... 2 more
[AUDIT ] CWWKZ0001I: Application fhir-server-webapp started in 150.635 seconds.
[ERROR ] The FHIR Server web application cannot process requests because it did not initialize correctly
The FHIR Server web application cannot process requests because it did not initialize correctly
Lee Surprenant (Aug 07 2020 at 21:07):
was it on the same system?
Lee Surprenant (Aug 07 2020 at 21:07):
if so, i'd expect similar results
Lee Surprenant (Aug 07 2020 at 21:10):
your options are:
- create the db before starting the server (we can give you steps); or
- increase the transaction timeout to see if it helps
Lee Surprenant (Aug 07 2020 at 21:11):
either way, if you could send output for lscpu and grep MemTotal /proc/meminfo and free -g that would be helpful so we can see what your system is working with (we're think maybe it is resource starved or something)
Purush Das (Aug 07 2020 at 21:13):
Yes. Same server(8 cores/16GB)..Could you provide steps to increase transaction timeout?
Lee Surprenant (Aug 07 2020 at 21:14):
either:
A. finding server.xml and adding this line in there:
<transaction totalTranLifetimeTimeout="480s" />
OR (for docker)
B. following the steps at https://hub.docker.com/r/ibmcom/ibm-fhir-server to specify a server.xml override
<server>
<logging traceSpecification="com.ibm.fhir.*=fine" traceFileName="stdout" />
<transaction totalTranLifetimeTimeout="480s" />
</server>
Lee Surprenant (Aug 07 2020 at 21:16):
by default, the transaction timeout is 120s
Purush Das (Aug 07 2020 at 21:35):
Increased timeout to 480s. Still same issues.
Here's the output of free memory and CPU
grep MemTotal /proc/meminfo
MemTotal: 16431692 kB
free -g
Mem: 15 4 0 0 11 10
Swap: 0 0 0
lscpu:
root@ubuntu16:/opt/ibm/fhir-server/wlp/usr/servers/fhir-server/logs# lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 8
On-line CPU(s) list: 0-7
Thread(s) per core: 1
Core(s) per socket: 1
Socket(s): 8
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 26
Model name: Intel(R) Xeon(R) CPU E5504 @ 2.00GHz
Stepping: 5
CPU MHz: 1995.000
BogoMIPS: 3990.00
Hypervisor vendor: VMware
Lee Surprenant (Aug 07 2020 at 21:36):
ok, one last ask: please add the logging line i place above (in option B). that will log a lot of debug stuff to the console
Lee Surprenant (Aug 07 2020 at 21:37):
then, either attach that output here or open an issue at https://github.com/ibm/fhir/issues and drop in there
Lee Surprenant (Aug 07 2020 at 21:37):
if you can do that, we'll get to the bottom of this
Lee Surprenant (Aug 07 2020 at 21:37):
thanks purush and have a good weekend
Purush Das (Aug 07 2020 at 21:43):
I did restart fhir-server after making timeout changes. Just now rebooted the server and started fhir-server. healthcheck is working. Probably, timeout changes did the trick. I will monitor and let you know if i face this issue again.
Thanks for all your help!
Have a nice weekend!
Digamber Kalivemula (Dec 08 2020 at 04:29):
when i tried to post a bundle of length: 20k+ resources I am getting below error. But i can post those resources successfully in small chunks like 1000 resources in a bundle at a time.
[12/8/20 4:24:08:540 UTC] 0000005a com.ibm.fhir.server.resources.FHIRResource E Commit global transaction failed. See server log for details
com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException: Commit global transaction failed. See server log for details [probeId=a-2c-0-1-3ea7a13d-c204-4abd-b597-e9b3568cf226]
at com.ibm.fhir.persistence.jdbc.connection.FHIRUserTransactionAdapter.end(FHIRUserTransactionAdapter.java:119)
at com.ibm.fhir.persistence.helper.FHIRTransactionHelper.commit(FHIRTransactionHelper.java:43)
at com.ibm.fhir.server.util.FHIRRestHelper.processBundleEntries(FHIRRestHelper.java:1520)
at com.ibm.fhir.server.util.FHIRRestHelper.doBundle(FHIRRestHelper.java:1078)
at com.ibm.fhir.server.resources.Batch.bundle(Batch.java:77)
at com.ibm.fhir.server.resources.Batch$Proxy$_$$_WeldClientProxy.bundle(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.ibm.ws.jaxrs20.cdi.component.JaxRsFactoryImplicitBeanCDICustomizer.serviceInvoke(JaxRsFactoryImplicitBeanCDICustomizer.java:339)
at com.ibm.ws.jaxrs20.server.LibertyJaxRsServerFactoryBean.performInvocation(LibertyJaxRsServerFactoryBean.java:641)
at com.ibm.ws.jaxrs20.server.LibertyJaxRsInvoker.performInvocation(LibertyJaxRsInvoker.java:160)
at org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:96)
at com.ibm.ws.jaxrs20.server.LibertyJaxRsInvoker.invoke(LibertyJaxRsInvoker.java:273)
at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:210)
at com.ibm.ws.jaxrs20.server.LibertyJaxRsInvoker.invoke(LibertyJaxRsInvoker.java:444)
at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:112)
at org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:61)
at org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:99)
at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:318)
at org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:123)
at org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:273)
at com.ibm.ws.jaxrs20.endpoint.AbstractJaxRsWebEndpoint.invoke(AbstractJaxRsWebEndpoint.java:136)
at com.ibm.websphere.jaxrs.server.IBMRestServlet.handleRequest(IBMRestServlet.java:146)
at com.ibm.websphere.jaxrs.server.IBMRestServlet.doPost(IBMRestServlet.java:104)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:706)
at com.ibm.websphere.jaxrs.server.IBMRestServlet.service(IBMRestServlet.java:96)
at com.ibm.ws.webcontainer.servlet.ServletWrapper.service(ServletWrapper.java:1230)
at com.ibm.ws.webcontainer.servlet.ServletWrapper.handleRequest(ServletWrapper.java:729)
at com.ibm.ws.webcontainer.servlet.ServletWrapper.handleRequest(ServletWrapper.java:426)
at com.ibm.ws.webcontainer.filter.WebAppFilterChain.invokeTarget(WebAppFilterChain.java:182)
at com.ibm.ws.webcontainer.filter.WebAppFilterChain.doFilter(WebAppFilterChain.java:93)
at com.ibm.fhir.server.filter.rest.FHIRRestServletFilter.doFilter(FHIRRestServletFilter.java:139)
at javax.servlet.http.HttpFilter.doFilter(HttpFilter.java:127)
at com.ibm.ws.webcontainer.filter.FilterInstanceWrapper.doFilter(FilterInstanceWrapper.java:201)
at com.ibm.ws.webcontainer.filter.WebAppFilterChain.doFilter(WebAppFilterChain.java:90)
at com.ibm.fhir.server.filter.rest.FHIRRestAuthorizationServletFilter.doFilter(FHIRRestAuthorizationServletFilter.java:86)
at com.ibm.ws.webcontainer.filter.FilterInstanceWrapper.doFilter(FilterInstanceWrapper.java:201)
at com.ibm.ws.webcontainer.filter.WebAppFilterChain.doFilter(WebAppFilterChain.java:90)
at com.ibm.ws.webcontainer.filter.WebAppFilterManager.doFilter(WebAppFilterManager.java:1001)
at com.ibm.ws.webcontainer.filter.WebAppFilterManager.invokeFilters(WebAppFilterManager.java:1139)
at com.ibm.ws.webcontainer.webapp.WebApp.handleRequest(WebApp.java:5037)
at com.ibm.ws.webcontainer.osgi.DynamicVirtualHost$2.handleRequest(DynamicVirtualHost.java:314)
at com.ibm.ws.webcontainer.WebContainer.handleRequest(WebContainer.java:1005)
at com.ibm.ws.webcontainer.osgi.DynamicVirtualHost$2.run(DynamicVirtualHost.java:279)
at com.ibm.ws.http.dispatcher.internal.channel.HttpDispatcherLink$TaskWrapper.run(HttpDispatcherLink.java:1134)
at com.ibm.ws.http.dispatcher.internal.channel.HttpDispatcherLink.wrapHandlerAndExecute(HttpDispatcherLink.java:415)
at com.ibm.ws.http.dispatcher.internal.channel.HttpDispatcherLink.ready(HttpDispatcherLink.java:374)
at com.ibm.ws.http.channel.internal.inbound.HttpInboundLink.handleDiscrimination(HttpInboundLink.java:577)
at com.ibm.ws.http.channel.internal.inbound.HttpInboundLink.handleNewRequest(HttpInboundLink.java:511)
at com.ibm.ws.http.channel.internal.inbound.HttpInboundLink.processRequest(HttpInboundLink.java:359)
at com.ibm.ws.http.channel.internal.inbound.HttpInboundLink.ready(HttpInboundLink.java:326)
at com.ibm.ws.channel.ssl.internal.SSLConnectionLink.determineNextChannel(SSLConnectionLink.java:1100)
at com.ibm.ws.channel.ssl.internal.SSLConnectionLink.readyInboundPostHandshake(SSLConnectionLink.java:757)
at com.ibm.ws.channel.ssl.internal.SSLConnectionLink$MyHandshakeCompletedCallback.complete(SSLConnectionLink.java:427)
at com.ibm.ws.channel.ssl.internal.SSLUtils.handleHandshake(SSLUtils.java:953)
at com.ibm.ws.channel.ssl.internal.SSLHandshakeIOCallback.complete(SSLHandshakeIOCallback.java:85)
at com.ibm.ws.tcpchannel.internal.WorkQueueManager.requestComplete(WorkQueueManager.java:504)
at com.ibm.ws.tcpchannel.internal.WorkQueueManager.attemptIO(WorkQueueManager.java:574)
at com.ibm.ws.tcpchannel.internal.WorkQueueManager.workerRun(WorkQueueManager.java:958)
at com.ibm.ws.tcpchannel.internal.WorkQueueManager$Worker.run(WorkQueueManager.java:1047)
at com.ibm.ws.threading.internal.ExecutorServiceImpl$RunnableWrapper.run(ExecutorServiceImpl.java:239)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:823)
0000005a com.ibm.fhir.server.filter.rest.FHIRRestServletFilter I Completed request[43.361 secs]: tenantId:[] dsId:[default] user:[fhiruser] method:[POST] uri:[*******] status:[500]
I tried:
1.Copied transaction-manager-long.xml from the WLP configDropins from /disabled to /overrides folder
2.adding <transaction totalTranLifeTimeout="480s"> in server.xml
Lee Surprenant (Dec 09 2020 at 20:17):
20k+ resources in a single transaction bundle is not advisable. for ingesting large amounts of resources, we'd recommend looking into the bulk import support: https://ibm.github.io/FHIR/guides/FHIRBulkOperations/#import-operation-dollarimport
Lee Surprenant (Dec 09 2020 at 20:17):
alternatively, you can look into our fhir-bucket project which has some utilities for splitting a large transaction bundle into many smaller ones (though very limited documentation at the moment)
Digamber Kalivemula (Dec 10 2020 at 04:26):
@Lee Surprenant Does this approaches support referencing?
Digamber Kalivemula (Dec 10 2020 at 12:07):
We are creating a bundle which will have resources referencing to each-other.We are using server created ID's for resources.Does this type of referencing work while using fhir-bucket to post data?
Lee Surprenant (Dec 10 2020 at 16:03):
@Digamber Kalivemula please only post in a single thread. can you please delete the duplicate post in #Literal-References ?
Last updated: Apr 12 2022 at 19:14 UTC
