topic Re: Has anybody parsed HL7 version 3 records (XML)? in Dashboards & Visualizations

Has anybody parsed HL7 version 3 records (XML)?

gregbo — Fri, 17 Mar 2017 13:27:31 GMT

I have some HL7 Version 3 records (XML) that I want to parse, but I'm having trouble figuring out how to do it. Some of the information is in a table format inside the record sort of like this (taken from a sample file):

            <component>
                <section>
                    <templateId root="2.16.840.1.113883.10.20.22.2.10"/>
                    <!--  **** Plan of Care section template  **** -->
                    <code code="18776-5" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Treatment plan"/>
                    <title>Plan of Care</title>
                    <text>
                        <table border="1" width="100%">
                            <thead>
                                <tr>
                                    <th>Planned Activity</th>
                                    <th>Planned Date</th>
                                </tr>
                            </thead>
                            <tbody>
                                <tr>
                                    <td>Colonoscopy</td>
                                    <td>April 21, 2000</td>
                                </tr>
                            </tbody>
                        </table>
                    </text>

I'd like to get the Plan of Care info and display it. Any way to do that?
I've tried using xpath, but it seems to not work at all.

Re: Has anybody parsed HL7 version 3 records (XML)?

woodcock — Fri, 17 Mar 2017 14:18:37 GMT

Using xpath is the way to go, I would start by stripping off layers and retrying. Also, you can extract fields from it on the way in using INDEXED_EXTRACTIONS=XML on the forwarder's props.conf, which I would definitely try.

Re: Has anybody parsed HL7 version 3 records (XML)?

gregbo — Mon, 20 Mar 2017 16:44:50 GMT

xpath is simply not working, even on tiny test files. Does anyone have any pointers for me, on where i can look for config issues or something?

Re: Has anybody parsed HL7 version 3 records (XML)?

woodcock — Tue, 21 Mar 2017 01:12:33 GMT

This fakes your data:

|makeresults|eval _raw="
<component>
   <section>
      <templateId root=\"2.16.840.1.113883.10.20.22.2.10\"/>
      <!--  **** Plan of Care section template  **** -->
      <code code=\"18776-5\" codeSystem=\"2.16.840.1.113883.6.1\" codeSystemName=\"LOINC\" displayName=\"Treatment plan\"/>
      <title>Plan of Care</title>
      <text>
         <table border=\"1\" width=\"100%\">
            <thead>
               <tr>
                  <th>Planned Activity</th>
                  <th>Planned Date</th>
               </tr>
            </thead>
            <tbody>
               <tr>
                  <td>Colonoscopy</td>
                  <td>April 21, 2000</td>
               </tr>
            </tbody>
         </table>
      </text>
   </section>
</component>"
| fields _time _raw

This is your solution:

| streamstats count AS _serial
| xpath "//component/section/text/table/thead/tr" outfield=thead
| xpath "//component/section/text/table/tbody/tr" outfield=tbody
| rex max_match=0 field=thead "(?ms)<th>(?<kvp_keys>[^\r\n]+)</th>"
| rex max_match=0 field=tbody "(?ms)<td>(?<kvp_values>[^\r\n]+)</td>"
| eval KVP=mvzip(kvp_keys, kvp_values, ":=:")
| fields _time KVP _serial
| mvexpand KVP
| rex field=KVP "^(?<kvp_key>.*):=:(?<kvp_value>.*)$"
| eval {kvp_key}=kvp_value
| fields - KVP _raw kvp_key kvp_value
| stats first(_time) AS _time values(*) AS * BY _serial

Re: Has anybody parsed HL7 version 3 records (XML)?

gregbo — Tue, 21 Mar 2017 09:34:04 GMT

I have tried those things, and I'm getting the same results. xpath seems to be failing silently, I haven't seen anything in the logs (even at DEBBUG).

Re: Has anybody parsed HL7 version 3 records (XML)?

gregbo — Tue, 21 Mar 2017 16:01:18 GMT

I found the problem I was having with xpath...turns out that one of the items in the header was preventing xpath from working;

<ClinicalDocument xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="urn:hl7-org:v3 http://xreg2.nist.gov:8080/hitspValidation/schema/cdar2c32/infrastructure/cda/C32_CDA.xsd"; xmlns="urn:hl7-org:v3" xmlns:mif="urn:hl7-org:v3/mif">

The next to last item (xmlns="urn:hl7-org:v3") caused the problem. If I take that out, xpath works as advertised.

Re: Has anybody parsed HL7 version 3 records (XML)?

meenu_2017 — Thu, 24 May 2018 18:41:16 GMT

Is INDEXED_EXTRACTIONS=XML setting still valid? I got an error for this setting in 7.0