Comments (5)
eedrummer
commented on August 13, 2024
Could you provide sample XML to reproduce this?
On Sunday, October 27, 2013, Ben West wrote:
When trying to upload a file in popHealth with an encounter section but no
dischargeDispositionCode, I get this error:Nokogiri::XML::XPath::SyntaxError (Undefined namespace prefix:
./sdtc:discharge\DispositionCode):
lib/record_importer.rb:64:in import'
app/controllers/admin_controller.rb:42:inblock (2 levels) in
upload_patients'
app/controllers/admin_controller.rb:39:in each'
app/controllers/admin_controller.rb:39:inblock in upload_patients'
app/controllers/admin_controller.rb:38:in `upload_patients'It seems to be coming from this line in health-data-standards:
encounter.discharge_disposition = extract_code(parent_element, "./sdtc:dischargeDispositionCode")
Encounters MAY contain [0..1] dischargeDispositionCodes, so the lack of a
dischargeDispositionCode shouldn't be a fatal error.—
Reply to this email directly or view it on GitHubhttps://github.com/projectcypress/health-data-standards/issues/64
.
from health-data-standards.
Xodarap
commented on August 13, 2024
I looked into this some more. I can't quite figure out the issue, but I think it has something to do with defining the sdtc namespace inline instead of at the top of the document. Below is a document which reproduces the issue - it's basically the same as the existing encounter performed test doc except I've defined sdtc inline and removed dischargeDisposition (and added some patient header stuff).
<?xml version="1.0" encoding="utf-8"?>
<?xml-stylesheet type='text/xsl' href='CDA.xsl'?>
<ClinicalDocument xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="urn:hl7-org:v3" xmlns:voc="urn:hl7-org:v3/voc" >
<realmCode code="US" />
<typeId extension="POCD_HD000040" root="2.16.840.1.113883.1.3" />
<templateId root="2.16.840.1.113883.10.20.24.1.1" />
<templateId root="2.16.840.1.113883.10.20.24.1.2" />
<id assigningAuthorityName="EPC" extension="4bca62ca-3d81-11e3-8ecc-460231621f93" root="1.2.840.114350.1.13.327.1.7.1.1" />
<code code="55182-0" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="QRDA Category I – Single Patient Report" />
<title>Quality Measure Report (Patient Level)</title>
<effectiveTime value="20131025092528" />
<confidentialityCode code="N" codeSystem="2.16.840.1.113883.5.25" />
<languageCode code="en-US" />
<recordTarget>
<patientRole>
<id extension="395-73-5097" root="2.16.840.1.113883.4.1" />
<addr use="HP">
<streetAddressLine nullFlavor="UNK" />
<city nullFlavor="UNK" />
</addr>
<telecom nullFlavor="UNK" />
<patient>
<name>
<given>crash</given>
<family>Btw</family>
</name>
<administrativeGenderCode code="F" codeSystem="2.16.840.1.113883.5.1" codeSystemName="AdministrativeGenderCode" />
<birthTime value="19631025" />
<ethnicGroupCode codeSystem="2.16.840.1.113883.6.238" nullFlavor="UNK" />
</patient>
</patientRole>
</recordTarget>
<legalAuthenticator>
<time value="20131025092528-0500" />
<signatureCode code="S" />
<assignedEntity>
<id extension="1000001143" root="2.16.840.1.113883.4.6" />
<telecom use="WP" />
<assignedPerson>
<name>
<given>MUHAMMAD</given>
<family>BTW AL-KHWARIZMI</family>
</name>
</assignedPerson>
<representedOrganization>
<id extension="1" root="1.2.840.114350.1.13.327.1.7.2.696570" />
<name>CDE FACILITY</name>
<telecom use="WP" value="tel:+1-404-777-8000" />
<addr nullFlavor="UNK" />
</representedOrganization>
</assignedEntity>
</legalAuthenticator>
<component>
<structuredBody>
<component>
<section>
<templateId root="2.16.840.1.113883.10.20.17.2.4" />
<templateId root="2.16.840.1.113883.10.20.24.2.1" />
<code code="55188-7" codeSystem="2.16.840.1.113883.6.1" />
<entry>
<encounter classCode="ENC" moodCode="EVN">
<templateId root="2.16.840.1.113883.10.20.22.4.49"/>
<templateId root="2.16.840.1.113883.10.20.24.3.23"/>
<id root="1.3.6.1.4.1.115" extension="512ba7eae7e915f677000003"/>
<code code="112689000" codeSystem="2.16.840.1.113883.6.96" sdtc:valueSet="2.16.840.1.113883.3.666.5.625" xmlns:sdtc="urn:hl7-org:sdtc"><originalText>Encounter, Performed: Hospital
Measures-Encounter Inpatient (Code List: 2.16.840.1.113883.3.666.5.625)</originalText></code>
<text>Encounter, Performed: Hospital Measures-Encounter Inpatient (Code List:
2.16.840.1.113883.3.666.5.625)</text>
<statusCode code="completed"/>
<effectiveTime>
<low value='20061121075239'/>
<high value='20061122012933'/>
</effectiveTime>
</encounter>
</entry>
</section>
</component>
</structuredBody>
</component>
</ClinicalDocument>
from health-data-standards.
eedrummer
commented on August 13, 2024
Thanks for the XML. I was able to reproduce the behavior that you were seeing.
The problem here is actually in the RecordImporter in popHealth. health-data-standards importers expect a Nokogiri document that has all of the namespace prefixes set up. In the RecordImporter, we were setting up the cda namespace prefix, but not the sdtc one. I think that on most documents, we could get away with that because Nokogiri will support any namespace prefixes that are declared in the start of the document. By registering the prefix, it fixes this bug.
I have the code working locally. I just need to package it up and issue a pull request.
I've added your XML example to the test suite. I hope you don't mind.
Additionally, we should probably rethink the assumptions health-data-standards makes about namespace prefixes being registered.
from health-data-standards.
Xodarap
commented on August 13, 2024
I've added your XML example to the test suite. I hope you don't mind.
Sure, no problem. Thanks for the quick turnaround.
from health-data-standards.
eedrummer
commented on August 13, 2024
Fixed in popHealth
from health-data-standards.
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