Inter-Server References

Jeff Eastman

unread,

Jul 13, 2016, 8:37:44 AM7/13/16

to HAPI FHIR

I have two HAPI-FHIR servers and have always believed that the full URL form of a Reference would work to support references between resources on the two servers. But when I try this I get e400. It would seem that a full URL form should be sufficient to support this capability.

Is there another mechanism, or do all server populations need to be independent?

Jeff

Jeff Eastman

unread,

Jul 13, 2016, 9:47:15 AM7/13/16

to HAPI FHIR

Digging deeper, it appears this should indeed be supported. From http://www.hl7.org/implement/standards/fhir/references.html:

"Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. Whether or not the reference is to a FHIR RESTful server, the reference SHALL point to a Resource as defined by this specification."

My absolute urls (e.g. http://52.72.172.54:8080/fhir/baseDstu2/Organization/Organization-1366) do match the regex and do resolve correctly to a resource on the public server, yet when I try to create a resource (e.g. a Contract) on my local server I get:

ca.uhn.fhir.rest.server.exceptions.InvalidRequestException: HTTP 400 Bad Request: Resource Organization/Organization-1366 not found, specified in path: Contract.actor.entity

From the message it would appear that my local server is not honoring the External Reference and is interpreting it as an Internal reference. Seems like a defect to me.

Jeff

Jeff Eastman

unread,

Jul 13, 2016, 12:00:28 PM7/13/16

to HAPI FHIR

Well, according to the documentation at http://hapifhir.io/doc_jpa.html, this behavior is the default but can be changed. Unfortunately, the documentation is out of date and the DaoConfig does not support the methods below. Grumble...

Jeff

By default, the server will reject this reference, as only local references are permitted by the server. This can be changed however.

If you want the server to recognize that this URL is actually a local reference (i.e. because the server will be deployed to the base URL http://example.com/fhir/) you can configure the server to recognize this URL via the following DaoConfig setting:

?

1

2

3

4

5

6

7

@Bean()

public DaoConfig daoConfig() {

    DaoConfig retVal = new DaoConfig();

    // ... other config ...

    retVal.getTreatBaseUrlsAsLocal().add("http://example.com/fhir/");

    return retVal;

}

On the other hand, if you want the server to be configurable to allow remote references, you can set this with the confguration below. Using the setAllowInlineMatchUrlReferences means that it will be possible to search for references that refer to these external references.

?

@Bean()

public DaoConfig daoConfig() {

    DaoConfig retVal = new DaoConfig();

    // Allow external references

    retVal.setAllowInlineMatchUrlReferences(true);

    // If you are allowing external references, it is recommended to

    // also tell the server which references actually will be local

    retVal.getTreatBaseUrlsAsLocal().add("http://mydomain.com/fhir");

    return retVal;

}

Kevin Mayfield

unread,

Jul 13, 2016, 12:54:29 PM7/13/16

to Jeff Eastman, HAPI FHIR

I've faced similar problems. We would have a doctor with regional ref of ABC but hapi ref will be 1234.

I've stuck with hapi refs as it gives referential integrity and that so makes searching more powerful. Downside is I have to convert requests/responses, not seeing that as too much of a problem.

Sent from my iPhone

--
You received this message because you are subscribed to the Google Groups "HAPI FHIR" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hapi-fhir+...@googlegroups.com.
To post to this group, send email to hapi...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/hapi-fhir/020f6943-95b4-4bc9-bb36-80aded9dd3e6%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

James Agnew

unread,

Jul 13, 2016, 1:23:53 PM7/13/16

to Jeff Eastman, HAPI FHIR

Hi Jeff,

The features/settings you quoted are presumably exactly what you need. Oddly enough they were added in the 1.6 release, which just came out. If you're still building against 1.5 you wouldn't see them.

Cheers,

James

--

You received this message because you are subscribed to the Google Groups "HAPI FHIR" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hapi-fhir+...@googlegroups.com.
To post to this group, send email to hapi...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/hapi-fhir/7ba5a04d-1085-48a7-abfc-06e3dbc9a27d%40googlegroups.com.

Jeff Eastman

unread,

Jul 13, 2016, 2:33:31 PM7/13/16

to HAPI FHIR, jdogs...@gmail.com

I've checked out the 1.6 release but cannot get it to build without testing failures. I did get a .war file but it will not start in Tomcat. Throws the following error:

13-Jul-2016 13:36:24.837 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to l

istener instance of class org.springframework.web.context.ContextLoaderListener

org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in ca.uhn.fhir.jpa.demo.FhirServerConfig: Invocation of init method failed; nested exception is org.hibernate.AnnotationException: @OneToOne or @ManyToOne on ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.myChild references an unknown entity: ca.uhn.fhir.jpa.entity.TermConcept

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1578)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:545)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)

at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)

at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)

at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)

at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)

at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1054)

at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:829)

at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:538)

at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:446)

at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:328)

at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)

at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4812)

at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5255)

at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:725)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:701)

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717)

at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:945)

at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1795)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:745)

Caused by: org.hibernate.AnnotationException: @OneToOne or @ManyToOne on ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.myChild references an unknown entity: ca.uhn.fhir.jpa.entity.TermConcept

at org.hibernate.cfg.ToOneFkSecondPass.doSecondPass(ToOneFkSecondPass.java:97)

at org.hibernate.boot.internal.InFlightMetadataCollectorImpl.processEndOfQueue(InFlightMetadataCollectorImpl.java:1787)

at org.hibernate.boot.internal.InFlightMetadataCollectorImpl.processFkSecondPassesInOrder(InFlightMetadataCollectorImpl.java:1730)

at org.hibernate.boot.internal.InFlightMetadataCollectorImpl.processSecondPasses(InFlightMetadataCollectorImpl.java:1617)

James Agnew

unread,

Jul 13, 2016, 3:47:40 PM7/13/16

to Jeff Eastman, HAPI FHIR

Wow, that's odd.

Do you mean that you are building HAPI itself from the git master? It is building successfully according to the CI server... Any chance it just needs an "mvn clean"?

Cheers,

James

To view this discussion on the web visit https://groups.google.com/d/msgid/hapi-fhir/9c5f7898-ef0b-4ff2-aef2-079876e4265a%40googlegroups.com.

Jeff Eastman

unread,

Jul 14, 2016, 8:23:20 AM7/14/16

to HAPI FHIR

I shut down Tomcat on port 8080, did a mvn clean install and the build failed here:

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO]

[INFO] HAPI-FHIR .......................................... SUCCESS [ 3.146 s]

[INFO] HAPI FHIR - Deployable Artifact Parent POM ......... SUCCESS [ 1.280 s]

[INFO] HAPI FHIR - Core Library ........................... SUCCESS [ 28.078 s]

[INFO] HAPI FHIR - Validation Resources (DSTU3) ........... SUCCESS [ 5.187 s]

[INFO] HAPI Tinder Plugin ................................. SUCCESS [ 14.238 s]

[INFO] HAPI FHIR Structures - DSTU1 (FHIR v0.80) .......... SUCCESS [01:02 min]

[INFO] HAPI FHIR - Validation Resources (DSTU2) ........... SUCCESS [ 5.650 s]

[INFO] HAPI FHIR Structures - DSTU2 (FHIR v1.0.0) ......... SUCCESS [01:02 min]

[INFO] HAPI FHIR - Minimal Dependency Test - Client ....... FAILURE [ 2.242 s]

[INFO] HAPI FHIR - Minimal Dependency Test - Server ....... SKIPPED

[INFO] HAPI Tinder Plugin - Test Project .................. SKIPPED

[INFO] HAPI FHIR Structures - HL7.org DSTU2 ............... SKIPPED

[INFO] HAPI FHIR Structures - DSTU3 ....................... SKIPPED

[INFO] HAPI FHIR JAX-RS Server ............................ SKIPPED

[INFO] HAPI FHIR JAX-RS Server - Example .................. SKIPPED

[INFO] HAPI FHIR JPA Server ............................... SKIPPED

[INFO] HAPI FHIR TestPage Overlay ......................... SKIPPED

[INFO] HAPI FHIR JPA Server - Example ..................... SKIPPED

[INFO] HAPI FHIR Sample RESTful Server .................... SKIPPED

[INFO] HAPI FHIR Sample RESTful Server - Tests ............ SKIPPED

[INFO] HAPI FHIR - fhirtest.uhn.ca Deployable WAR ......... SKIPPED

[INFO] HAPI FHIR - Android ................................ SKIPPED

[INFO] HAPI FHIR - Command Line Client - Base Project ..... SKIPPED

[INFO] HAPI FHIR - Command Line Client - Server WAR ....... SKIPPED

[INFO] HAPI FHIR - Command Line Client - Application ...... SKIPPED

[INFO] HAPI FHIR - Distribution Archive ................... SKIPPED

[INFO] HAPI FHIR - Examples (for site) .................... SKIPPED

[INFO] hapi-fhir-base-example-embedded-ws ................. SKIPPED

[INFO] HAPI FHIR - JaCoCo Test Coverage ................... SKIPPED

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 03:05 min

[INFO] Finished at: 2016-07-14T08:17:18-04:00

[INFO] Final Memory: 81M/580M

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.19.1:test (default-test) on project hapi-fhir-base-testmindeps-client: There are test failures.

Looks like this test failed:

-------------------------------------------------------------------------------

Test set: ca.uhn.fhir.rest.client.ClientTest

-------------------------------------------------------------------------------

Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.818 sec <<< FAILURE! - in ca.uhn.fhir.rest.client.ClientTest

testTransaction(ca.uhn.fhir.rest.client.ClientTest) Time elapsed: 0.753 sec <<< ERROR!

ca.uhn.fhir.rest.client.exceptions.NonFhirResponseException: Response contains non FHIR Content-Type 'text/html' : <html><head><meta http-equiv="refresh" content="0;url=http://www.dnsrsearch.com/index.php?origURL=http://this_is_an_invalid_host_name_yes_it_is/fhir/metadata&bc="/></head><body><script type="text/javascript">window.location="http://www.dnsrsearch.com/index.php?origURL="+escape(window.location)+"&r="+escape(document.referrer)+"&bc=";</script></body></html>

at ca.uhn.fhir.rest.client.ClientTest.testTransaction(ClientTest.java:25)

and

<error message="Response contains non FHIR Content-Type 'text/html' : <html><head><meta http-equiv="refresh" content="0;url=http://www.dnsrsearch.com/index.php?origURL=http://this_is_an_invalid_host_name_yes_it_is/fhir/metadata&bc="/></head><body><script type="text/javascript">window.location="http://www.dnsrsearch.com/index.php?origURL="+escape(window.location)+"&r="+escape(document.referrer)+"&bc=";</script></body></html>" type="ca.uhn.fhir.rest.client.exceptions.NonFhirResponseException"><![CDATA[ca.uhn.fhir.rest.client.exceptions.NonFhirResponseException: Response contains non FHIR Content-Type 'text/html' : <html><head><meta http-equiv="refresh" content="0;url=http://www.dnsrsearch.com/index.php?origURL=http://this_is_an_invalid_host_name_yes_it_is/fhir/metadata&bc="/></head><body><script type="text/javascript">window.location="http://www.dnsrsearch.com/index.php?origURL="+escape(window.location)+"&r="+escape(document.referrer)+"&bc=";</script></body></html>

at ca.uhn.fhir.rest.client.ClientTest.testTransaction(ClientTest.java:25)

]]></error>

<system-err><![CDATA[7 [main] INFO ca.uhn.fhir.util.VersionUtil - HAPI FHIR version is: 1.6

21 [main] INFO ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [DSTU1]

769 [main] WARN ca.uhn.fhir.rest.client.apache.ApacheHttpResponse - Response did not specify a charset.

]]></system-err>

</testcase>

Jeff Eastman

unread,

Jul 14, 2016, 9:11:31 AM7/14/16

to HAPI FHIR, jdogs...@gmail.com

NVM. Its building just fine on my AWS Linux servers. The problem seems to be local to my Mac OS X El Capitan laptop.

Jeff

James Agnew

unread,

Jul 14, 2016, 9:20:12 AM7/14/16

to Jeff Eastman, HAPI FHIR

Hi Jeff,

Oddly enough I was typing a response as yours came in. Glad it's working for you in one environment at least!

That error looks like DNS issues trying to resolve a name that is deliberately wrong in the test, e.g:

Response contains non FHIR Content-Type 'text/html' : <html><head><meta http-equiv="refresh" content="0;url=http://www.dnsrsearch.com/index.php?origURL=http://this_is_an_invalid_host_name_yes_it_is/fhir/metadata&bc="/>

This particular name (http://this_is_an_invalid_host_name_yes_it_is) gives a connection error when I run it, but probably you are running in an environment where your ISP tries to be helpful by serving up an HTTP page.

I've just committed a fix to not use a DNS name for that test- any chance you could update and try once more on the machine that was failing?

Cheers,

James

To view this discussion on the web visit https://groups.google.com/d/msgid/hapi-fhir/ef857a7e-88f1-4dc3-9c39-ef8b893a17a5%40googlegroups.com.

Jeff Eastman

unread,

Jul 14, 2016, 10:40:33 AM7/14/16

to HAPI FHIR

I've been able to build v1.6 on AWS and, by setting FhirServerConfig.java to allowExternalReferences, am able to store resources containing external references to resources in our public HAPI-FHIR server (http://52.72.172.54:8080/fhir/home).

Thanks James!

Jeff

/**

* Configure FHIR properties around the the JPA server via this bean

*/

@Bean()

public DaoConfig daoConfig() {

DaoConfig retVal = new DaoConfig();

retVal.setSubscriptionEnabled(true);

retVal.setSubscriptionPollDelay(5000);

retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);

retVal.setAllowMultipleDelete(true);

retVal.setAllowExternalReferences(true);

return retVal;

}

Jeff Eastman

unread,

Jul 14, 2016, 3:11:44 PM7/14/16

to HAPI FHIR

Well it build fine on Mac OS X this time. Maybe the timeout last time was a transient.

[INFO] HAPI-FHIR .......................................... SUCCESS [ 3.745 s]

[INFO] HAPI FHIR - Deployable Artifact Parent POM ......... SUCCESS [ 1.128 s]

[INFO] HAPI FHIR - Core Library ........................... SUCCESS [ 28.758 s]

[INFO] HAPI FHIR - Validation Resources (DSTU3) ........... SUCCESS [ 5.400 s]

[INFO] HAPI Tinder Plugin ................................. SUCCESS [ 16.276 s]

[INFO] HAPI FHIR Structures - DSTU1 (FHIR v0.80) .......... SUCCESS [ 58.646 s]

[INFO] HAPI FHIR - Validation Resources (DSTU2) ........... SUCCESS [ 3.323 s]

[INFO] HAPI FHIR Structures - DSTU2 (FHIR v1.0.0) ......... SUCCESS [ 50.994 s]

[INFO] HAPI FHIR - Minimal Dependency Test - Client ....... SUCCESS [ 1.142 s]

[INFO] HAPI FHIR - Minimal Dependency Test - Server ....... SUCCESS [ 2.706 s]

[INFO] HAPI Tinder Plugin - Test Project .................. SUCCESS [ 8.357 s]

[INFO] HAPI FHIR Structures - HL7.org DSTU2 ............... SUCCESS [01:56 min]

[INFO] HAPI FHIR Structures - DSTU3 ....................... SUCCESS [01:15 min]

[INFO] HAPI FHIR JAX-RS Server ............................ SUCCESS [ 9.807 s]

[INFO] HAPI FHIR JAX-RS Server - Example .................. SUCCESS [ 7.498 s]

[INFO] HAPI FHIR JPA Server ............................... SUCCESS [05:01 min]

[INFO] HAPI FHIR TestPage Overlay ......................... SUCCESS [ 7.672 s]

[INFO] HAPI FHIR JPA Server - Example ..................... SUCCESS [ 21.964 s]

[INFO] HAPI FHIR Sample RESTful Server .................... SUCCESS [ 10.796 s]

[INFO] HAPI FHIR Sample RESTful Server - Tests ............ SUCCESS [ 4.755 s]

[INFO] HAPI FHIR - fhirtest.uhn.ca Deployable WAR ......... SUCCESS [ 4.076 s]

[INFO] HAPI FHIR - Android ................................ SUCCESS [ 11.357 s]

[INFO] HAPI FHIR - Command Line Client - Base Project ..... SUCCESS [ 0.006 s]

[INFO] HAPI FHIR - Command Line Client - Server WAR ....... SUCCESS [ 5.432 s]

[INFO] HAPI FHIR - Command Line Client - Application ...... SUCCESS [ 18.067 s]

[INFO] HAPI FHIR - Distribution Archive ................... SUCCESS [ 0.018 s]

[INFO] HAPI FHIR - Examples (for site) .................... SUCCESS [ 1.248 s]

[INFO] hapi-fhir-base-example-embedded-ws ................. SUCCESS [ 0.234 s]

[INFO] HAPI FHIR - JaCoCo Test Coverage ................... SUCCESS [ 40.071 s]

[INFO] ------------------------------------------------------------------------

[INFO] BUILD SUCCESS

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 13:37 min

[INFO] Finished at: 2016-07-14T15:10:30-04:00

[INFO] Final Memory: 162M/795M

[INFO] ------------------------------------------------------------------------

kuladeep kumar

unread,

Jul 20, 2016, 3:41:26 PM7/20/16

to HAPI FHIR

Hi

I was trying to setup HAPI server on AWS ubuntu instance. I did a mvn clean install and built the packages successfully on Windows 7 machine. And FTPed the hapi-fhir-jpaserver-example.war to my AWS ubuntu Instance and moved it to webapps folder(in Tomcat7). I am not able to start hapi-fhir-jpaserver-example application from manager gui. I have attached the tomcat logs.. Could you please suggest me a resolution.. Many Thanks.

ERROR XBM0H: Directory /var/lib/tomcat7/target/jpaserver_derby_files cannot be created.

at org.apache.derby.iapi.error.StandardException.newException(Unknown Source)

Best Regards

Kuladeep

catalina.out

localhost.2016-07-20.log

James Agnew

unread,

Jul 20, 2016, 3:54:55 PM7/20/16

to kuladeep kumar, HAPI FHIR

This just means that the user that Tomcat is running under does not have write access to create the directory "/var/lib/tomcat7/target/jpaserver_derby_files".

You have a few options here:

* Configure Hibernate to talk to a different database (e.g. Postgres)

* Create that directory and give your tomcat user write access to it

* Change the configuration so that instead of "target/jpaserver_derby_files" it puts its files somewhere else.

Cheers,

James

--

You received this message because you are subscribed to the Google Groups "HAPI FHIR" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hapi-fhir+...@googlegroups.com.
To post to this group, send email to hapi...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/hapi-fhir/79cc3ba2-4022-4658-a457-96446b1264b3%40googlegroups.com.

Alan Macaluso

unread,

Aug 11, 2017, 5:50:43 PM8/11/17

to HAPI FHIR, kumar.k...@gmail.com

I'm getting similar errors but on DSTU3 structure. Building on OSX 10.10.5. I've tried building on various AWS AMIs as well with varying degrees of failure:

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO]

[INFO] HAPI-FHIR .......................................... SUCCESS [ 1.039 s]

[INFO] HAPI FHIR - Deployable Artifact Parent POM ......... SUCCESS [ 0.714 s]

[INFO] HAPI FHIR - Core Library ........................... SUCCESS [ 15.889 s]

[INFO] HAPI Tinder Plugin ................................. SUCCESS [ 21.791 s]

[INFO] HAPI FHIR Structures - DSTU1 (FHIR v0.80) .......... SUCCESS [ 52.649 s]

[INFO] HAPI FHIR - Validation Resources (DSTU2) ........... SUCCESS [ 3.183 s]

[INFO] HAPI FHIR Structures - DSTU2 (FHIR v1.0.0) ......... SUCCESS [ 44.251 s]

[INFO] HAPI FHIR - Minimal Dependency Test - Client ....... SUCCESS [ 1.477 s]

[INFO] HAPI FHIR - Minimal Dependency Test - Server ....... SUCCESS [ 2.982 s]

[INFO] HAPI FHIR - Validation Resources DSTU2.1 (2016May) . SUCCESS [ 3.083 s]

[INFO] HAPI FHIR Structures - DSTU2.1 (2016May) ........... SUCCESS [01:00 min]

[INFO] HAPI FHIR - Validation Resources (DSTU3) ........... SUCCESS [ 3.566 s]

[INFO] HAPI FHIR Structures - DSTU3 ....................... FAILURE [01:53 min]