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Vexing issues with CDM v5 vocabulary files

Vocabulary Users
#21

@Christian_Reich: re: “Well, the first is really a dumb code: “Apparent life threatening event in infant”. How do you do analytics on that?” Term of art - think of it as “chest pain” for infants.

For additional analytic fun, what I’ll call “sociology” is keeping the diagnostic landscape interesting: ALTEs are now officially BRUEs (http://emedicine.medscape.com/article/1418765-overview). But I trust in the ability of concept_relationship to iron out the bumps between “near-SIDS”, “ALTE”, and “BRUE” and make standard analytics possible. :slight_smile:

#22

Interesting. I learned something new.

#23

Yes. It’s passing Oracle constraints requiring a concept_id for concept_relationships. Can you give us the list it prints?

#24

I tracked down the problem. On Linux:

java -jar cpt4.jar

does not properly append to CONCEPT.csv, but rather produces a lower-case concept.csv. I thought this problem had been fixed, per this post. If I append concept.csv to CONCEPT.csv, the problems with CONCEPT_RELATIONSHIP.csv, CONCEPT_ANCESTOR.csv, and CONCEPT_SYNONYM.csv having terms that do not appear in CONCEPT.csv go away.

1 Like
#25

@Christophe_Lambert:

Ah. Regression problem. Sorry about that. Glad it works. Keep it coming.

We are still on the NDC problem, but it looks like that RxNorm made a change to prefabricated injectables (like syringes with the substance in there as powder): Instead of the concentration they provide the total amount. They provide new codes for these and proper upgrades for the old ones, but only for those that are currently prescribable. I am still finding out and will as RxNorm what’s going on. It may take a little.

1 Like
#26

We have examples of the condition codes from various site’s source data in our network that currently have a deprecated mapping in concept_relationship. Would you like us to send you our full list for your team to investigate?

#27

@burrowse: Be so kind.

#28

Hi @Christian_Reich,

I believe cpt4.jar is either broken again, or there is a problem with the server side. I downloaded the vocabulary with the default vocabularies on 6/12/2016, and got this error:

$java -jar cpt4.jar 5
Exception in thread "main" com.sun.xml.internal.ws.fault.ServerSOAPFaultException: Client received SOAP Fault from server: Java heap space Please see the server log to find more detail regarding exact cause of the failure.
at com.sun.xml.internal.ws.fault.SOAP11Fault.getProtocolException(SOAP11Fault.java:178)
at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(SOAPFaultBuilder.java:116)
at com.sun.xml.internal.ws.client.sei.StubHandler.readResponse(StubHandler.java:238)
at com.sun.xml.internal.ws.db.DatabindingImpl.deserializeResponse(DatabindingImpl.java:189)
at com.sun.xml.internal.ws.db.DatabindingImpl.deserializeResponse(DatabindingImpl.java:276)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:104)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:77)
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:147)
at com.sun.proxy.$Proxy34.getCode(Unknown Source)
at org.odhsi.utils.cpt.Application.process(Application.java:113)
at org.odhsi.utils.cpt.Application.main(Application.java:84)

Has anyone else had this problem? It occurs on both Windows and Linux.

v5.0 08-JUN-16
#29

Hello @Christophe_Lambert!

Can you try to run it with “java -Xmx512M -XX:MaxPermSize=128m -jar cpt4.jar 5”?

#30

It now works both with and without specifying the extra command line arguments. Perhaps it was an intermittent issue with the server.

#31

@Vladimir_Nikolaenko:

Can we improve the error messaging of the utility? The dump of the stack is probably not that useful.

#32

@Vladimir_Nikolaenko
Also, I was surprised to see that when running the cpt4.jar two times on the same data I got the 14580 CPT4 codes tacked onto the CONCEPT.csv file in a different order each time. I would recommend that it be stable from one run to the next – perhaps printing them out in the same order as they appear in CONCEPT_CPT4.csv. That way, we can readily run a diff between changing versions of vocabularies. Note: I am not 100% sure that it is not a matter of CONCEPT_CPT4.csv coming back in two different orders (sorry).

#33

Yes, we’ll do

#34

Thx, we’ll think about it

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