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v5.0 08-JUN-16

Vocabulary Users
#1

I am very glad to see vocabulary release with updated RxNorm.

After downloading the .zip file and trying to run the CPT4 step, I am getting the following error:
(I had no issues with prior versions (e.g., April 2016))

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(Unknown Source)
    at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(Unknown Source)
    at com.sun.xml.internal.ws.client.sei.StubHandler.readResponse(Unknown Source)
    at com.sun.xml.internal.ws.db.DatabindingImpl.deserializeResponse(Unknown Source)
    at com.sun.xml.internal.ws.db.DatabindingImpl.deserializeResponse(Unknown Source)
    at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source)
    at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source)
    at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(Unknown Source)
    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)

Could that be just my firewall? (again, it worked fine 2 months ago)
Can someone reply if they were able to run the CPT JAR step (on Windows) on the above release?
What can I do to eliminate this error?
Which Soap server it is trying to call (and what port should I ask the admins to allow? (perhaps?)

#2

@Vojtech_Huser:

Thanks, man. Will debug.

#3

@Christophe_Lambert reports same problem:

#4

thank you for fixing it. error is gone in Jun-20 version.

#5

I just noticed something strange. I am using “surgery” concepts as descendants of SNOMED “Surgical Procedure” 4301351 or MedRA “Surgery” 37522270.
In previous version (v5.0 2014-10-15) the number of valid concepts was as follows:

Vocab_id	Count
CPT4		4084
HCPCS		  97
MedDRA		   3
SNOMED	       18438

When I run the same query on the new version (v5.0 08-JUN-16), I am getting drastically different vocabularies and counts:

Vocab_id	Count
HCPCS		 206
ICD9Proc	7074
MedDRA		   6
OPCS4		8628
SNOMED	       41102

The query itself is very simple:

SELECT vocabulary_id, count(*) FROM omopv5.concept a 
JOIN omopv5.concept_ancestor b ON b.descendant_concept_id = a.concept_id 
WHERE a.valid_end_date > sysdate AND b.ancestor_concept_id in (4301351,37522270) 
GROUP BY vocabulary_id ORDER BY 1;

Am I missing something obvious?

#6

The expansion of vocabularies and concepts is not surprising…the OHDSI
vocabulary team has made great strides in improving both the depth and
breadth of the vocabularies and mappings during the 2 years between the
vocabularies you are comparing. What does look like a miss is that you
don’t have CPT4 in your newer vocabulary result…that should be there, and
I do in fact see it in my current vocab using the same query. Here’s my
results running on my version of vocab v5.0 20-JUN-16:

vocabulary_id count
CPT4 8866
HCPCS 206
ICD9Proc 7074
MedDRA 6
OPCS4 8628
SNOMED 41269

So one thing you might want to check: did you download the vocabulary with
CPT4 included, and then run the CPT4 augmenter tool afterwards? While you
are at it, you might want to get the latest vocabulary…it’s constantly
improving, …

Vocabulary changes between versions
#7

@Patrick_Ryan: Thank you!

Vocabulary changes between versions
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