Does custom Search Parameter work retrospectively on resources

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Ajay shekar

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Mar 8, 2021, 8:56:17 AM3/8/21

to HAPI FHIR

Hello All,

I am using hapi-fhir-jpaserver-starter 5.3.0 with Partitioning being enabled.

If i create a custom Search Parameter after creating some resources, then I cannot search resources which are previously created.

Is there any option to get the search results retrospectively ?

Eg: If i create a custom SP -

PUT - http://localhost:8080/fhir/DEFAULT/SearchParameter/pract-org

{

"resourceType": "SearchParameter",

"id":"pract-org",

"title": "Org Id",

"base": [ "Practitioner" ],

"status": "active",

"code": "organization",

"type": "reference",

"expression": "Practitioner.extension('http://xxx.com/Organization')",

"xpathUsage": "normal"

}

Then with search query GET http://localhost:8080/fhir/DEFAULT/SearchParameter?organization=Organization/1

1. I only get the practitioner resource linked to Organization/1, which were created after creation of custom SP (SearchParameter/pract-org).

2. Can i search Practitioner resource linked to Organization/1, which were created before custom SP getting created ?

James Agnew

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Mar 8, 2021, 8:59:54 AM3/8/21

to Ajay shekar, HAPI FHIR

You can request a manual reindex of all your data by POST-ing to the following URL:

http://[server_base]/$mark-all-resources-for-reindexing

Cheers,

James

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Ajay shekar

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Mar 11, 2021, 1:58:55 PM3/11/21

to HAPI FHIR

Thanks James for the reply.

But when i try to perform http://[server_base]/$mark-all-resources-for-reindexing I am getting storage partition read error or even if I update a search parameter it automatically tries to re-index the previous concerned resources and throw following error.

The problem is there is no Partition related information when it is trying to access a resource for reindexing @ https://github.com/hapifhir/hapi-fhir/blob/master/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/RequestPartitionHelperSvc.java#L95.

determineReadPartitionForRequest(@Nullable RequestDetails theRequest, String theResourceType) theRequest shouldn't be null but it receives null during reindexing.

The error:

2021-03-12 00:12:49.754 [qtp338027825-33] INFO fhirtest.access [LoggingInterceptor.java:175] Path[/fhir] Source[] Operation[extended-operation-server $mark-all-resources-for-reindexing ] UA[PostmanRuntime/7.26.8] Params[?type=Practitioner] ResponseEncoding[JSON] Operation[extended-operation-server $mark-all-resources-for-reindexing ] UA[PostmanRuntime/7.26.8] Params[?type=Practitioner] ResponseEncoding[JSON]

2021-03-12 00:12:54.579 [hapi-fhir-jpa-scheduler-clustered-3] INFO c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:309] Running 1 reindex jobs: [ResourceReindexJobEntity[id=110,resourceType=<null>,thresholdLow=<null>,thresholdHigh=2021-03-12 00:17:49.748]]

2021-03-12 00:12:54.580 [hapi-fhir-jpa-scheduler-clustered-3] INFO c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:359] Performing reindex pass for JOB[110]

2021-03-12 00:13:46.042 [HikariPool-1 housekeeper] WARN com.zaxxer.hikari.pool.HikariPool [HikariPool.java:668] HikariPool-1 - Thread starvation or clock leap detected (housekeeper delta=1m3s70ms461µs475ns).

2021-03-12 00:14:17.412 [hapi-fhir-jpa-scheduler-clustered-3] INFO c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:389] Loaded 3 resources for reindexing in 4ms

2021-03-12 00:14:51.496 [ResourceReindex-9] ERROR c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:579] Failed to index resource Practitioner/1/_history/1: ca.uhn.fhir.rest.server.exceptions.InternalErrorException: No interceptor provided a value for pointcut: STORAGE_PARTITION_IDENTIFY_READ

ca.uhn.fhir.rest.server.exceptions.InternalErrorException: No interceptor provided a value for pointcut: STORAGE_PARTITION_IDENTIFY_READ

at ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc.validateRequestPartitionNotNull(RequestPartitionHelperSvc.java:285)

at ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc.determineReadPartitionForRequest(RequestPartitionHelperSvc.java:114)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.readEntity(BaseHapiFhirResourceDao.java:1145)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.readEntity(BaseHapiFhirResourceDao.java:1131)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.doRead(BaseHapiFhirResourceDao.java:1088)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.lambda$read$9(BaseHapiFhirResourceDao.java:1074)

at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)

at ca.uhn.fhir.jpa.dao.tx.HapiTransactionService.execute(HapiTransactionService.java:65)

at ca.uhn.fhir.jpa.dao.tx.HapiTransactionService.execute(HapiTransactionService.java:56)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.read(BaseHapiFhirResourceDao.java:1074)

at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.base/java.lang.reflect.Method.invoke(Method.java:566)

at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)

at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)

at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)

at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137)

at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)

at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:215)

at com.sun.proxy.$Proxy249.read(Unknown Source)

at ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl$ResourceReindexingTask.lambda$call$0(ResourceReindexingSvcImpl.java:563)

at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)

at ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl$ResourceReindexingTask.call(ResourceReindexingSvcImpl.java:544)

at ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl$ResourceReindexingTask.call(ResourceReindexingSvcImpl.java:519)

at java.base/java.util.concurrent.FutureTask.run$$$capture(FutureTask.java:264)

at java.base/java.util.concurrent.FutureTask.run(FutureTask.java)

at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

at java.base/java.lang.Thread.run(Thread.java:834)

2021-03-12 00:14:54.723 [ResourceReindex-9] INFO c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:598] Setting resource PID[1] status to ERRORED

2021-03-12 00:14:54.724 [ResourceReindex-9] INFO c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:467] Marking resource with PID 1 as indexing_failed

2021-03-12 00:14:55.344 [qtp338027825-27] INFO c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:236] Marking all resources of type Practitioner for reindexing - Got job ID[111]

2021-03-12 00:14:55.351 [qtp338027825-27] INFO c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:236] Marking all resources of type StructureDefinition for reindexing - Got job ID[112]

2021-03-12 00:15:18.600 [ResourceReindex-9] ERROR c.u.f.j.s.r.ResourceReindexingSvcImpl [ResourceReindexingSvcImpl.java:579] Failed to index resource Practitioner/52/_history/1: ca.uhn.fhir.rest.server.exceptions.InternalErrorException: No interceptor provided a value for pointcut: STORAGE_PARTITION_IDENTIFY_READ