FHIR Chat · how to filter by abstract codes? · terminology

Stream: terminology

Topic: how to filter by abstract codes?

Eric Haas (Jul 14 2020 at 18:25):

the CLD for the value set "all non-abstract codes"

I don't know how to do this. I looked and did not see a way.

John Moehrke (Jul 14 2020 at 18:40):

is it .contains.abstract false?

Eric Haas (Jul 14 2020 at 19:21):

Its some filter

 <include>  <!-- 1..* Include one or more codes from a code system or other value set(s) -->
   <system value="[uri]"/><!-- ?? 0..1 The system the codes come from -->
   <filter>  <!-- ?? 0..* Select codes/concepts by their properties (including relationships) -->
    <property value="[code]"/><!-- 1..1 A property/filter defined by the code system -->
    <op value="[code]"/><!-- 1..1 = | is-a | descendent-of | is-not-a | regex | in | not-in | generalizes | exists -->
    <value value="[string]"/><!-- 1..1 Code from the system, or regex criteria, or boolean value for exists -->
   </filter>
</include

John Moehrke (Jul 14 2020 at 20:11):

Moehrke Research (@John Moehrke and @ryan moehrke ) have failed, trying all kinds of .filter mechanics.

Grahame Grieve (Jul 14 2020 at 20:27):

so the first thing to do is to make sure that the code system actually defines what is abstract or not. Here's what's required, for Eric's code system of focus:

Grahame Grieve (Jul 14 2020 at 20:27):

https://github.com/FHIR/packages/commit/04d4796595f55769756e6e36ebcffda514e4d909

Grahame Grieve (Jul 14 2020 at 20:28):

having done that, then you write a filter based on the notSelectable property:

Grahame Grieve (Jul 14 2020 at 20:29):

<filter>
  <property value="abstract"/>
  <op value="="/>
  <value value="false"/>
</filter>

John Moehrke (Jul 14 2020 at 20:36):

I tried that

John Moehrke (Jul 14 2020 at 20:39):

which according to http://build.fhir.org/codesystem.html#filters we should not need to add that filter as all properties magically include the "=" and "in"... but I tried it anyway

John Moehrke (Jul 14 2020 at 20:44):

I have also tried including the codeSystem, and then exclude the codeSystem with filter of notSelectable.. got nothing expanded at all

Grahame Grieve (Jul 14 2020 at 20:45):

according to http://build.fhir.org/codesystem.html#filters we should not need to add that filter as all properties magically include the "=" and "in"...

I have no idea what that means

John Moehrke (Jul 14 2020 at 21:42):

well, I didn't trust that statement in the FHIR spec either.. hence why I tried it explicitly.

John Moehrke (Jul 15 2020 at 18:25):

@Eric Haas did yo get this working? I have tried other things still not working.

John Moehrke (Jul 16 2020 at 14:46):

@Grahame Grieve can you help me? when I use any filter I get no expansion. I have even tried to include and exclude. My repo is https://github.com/IHE/FormatCode

Eric Haas (Jul 16 2020 at 21:39):

It is not working for me either

Michael Lawley (Jul 16 2020 at 21:45):

It means that for every property, there is an (implicit) filter with (at least) those two operators

Michael Lawley (Jul 16 2020 at 21:47):

@John Moehrke does it work if you use a different terminology server?

John Moehrke (Jul 16 2020 at 22:00):

I don't know how to do that

Michael Lawley (Jul 16 2020 at 22:01):

You can call the igpublisher with -tx and the URL for another tx server. Eg https://r4.ontoserver.csiro.au/fhir

Grahame Grieve (Jul 17 2020 at 05:45):

@John Moehrke what have you tried? Have you cleaned out the cache?

John Moehrke (Jul 17 2020 at 11:13):

I have not tried cleaning the cache, which cache shall I clean with what detergent?

Grahame Grieve (Jul 17 2020 at 11:17):

you have a txCache. Delete the files in there

Grahame Grieve (Jul 17 2020 at 11:17):

oh. I know why you mightn't be seeing that. I'll have to debug

Grahame Grieve (Jul 17 2020 at 11:17):

is what you have committed to master?

John Moehrke (Jul 17 2020 at 11:21):

yes

Grahame Grieve (Jul 17 2020 at 11:29):

ok I'll look tomorrow

John Moehrke (Jul 17 2020 at 11:33):

cleaning the txCache did not help

Michael Lawley (Jul 17 2020 at 22:20):

This is what I see the in txcache (when using Ontoserver):

{"hierarchical" : true, "valueSet" :{
  "resourceType" : "ValueSet",
  "compose" : {
    "include" : [{
      "system" : "http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode",
      "filter" : [{
        "property" : "notSelectable",
        "op" : "=",
        "value" : "false"
      }]
    }]
  }
}}####
e: {
  "error" : "Error from server: Error:org.hl7.fhir.r5.model.CodeableConcept@a357c3e\r\n"
}

the default Tx has the error text as:
"error" : "Error from server: Unable to provide support for code system http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode"

Grahame Grieve (Jul 18 2020 at 03:39):

it's an issue in the publisher's mini terminology server

Grahame Grieve (Jul 20 2020 at 22:24):

fixed next release

John Moehrke (Jul 27 2020 at 18:15):

I don't think this is working yet. @Eric Haas did you get yours working?

Eric Haas (Jul 28 2020 at 22:22):

not yet

Grahame Grieve (Jul 28 2020 at 22:23):

the code is certainly working ...

John Moehrke (Jul 29 2020 at 13:24):

teach me

John Moehrke (Jul 29 2020 at 13:24):

You @Grahame Grieve have full access to my FormatCode IG.

Eric Haas (Aug 04 2020 at 20:08):

here is my ValueSet"

<?xml version="1.0" encoding="UTF-8"?>
<ValueSet xmlns="http://hl7.org/fhir" xmlns:xhtml="http://www.w3.org/1999/xhtml">
  <id value="us-core-provider-specialty"/>
  <url value="http://hl7.org/fhir/us/core/ValueSet/us-core-provider-specialty"/>
  <version value="1.0.1"/>
  <name value="USCoreProviderSpecialityNucc"/>
  <title value="US Core Provider Speciality (NUCC)"/>
  <status value="active"/>
  <date value="2019-05-21"/>
  <publisher value="HL7 US Realm Steering Committee"/>
  <contact>
    <telecom>
      <system value="other"/>
      <value value="http://hl7.org/fhir"/>
    </telecom>
  </contact>
  <description value="Provider speciality roles codes which are composed of the NUCC Health Care Provider Taxonomy Code Set for providers"/>
  <copyright value="This value set includes content from NUCC Health Care Provider Taxonomy Code Set for providers which is copyright © 2016+ American Medical Association.  For commercial use, including sales or licensing, a license must be obtained."/>
  <compose>
    <include>
      <system value="http://nucc.org/provider-taxonomy"/>
      <filter>
        <property value="abstract"/>
        <op value="="/>
        <value value="false"/>
      </filter>
    </include>
  </compose>
</ValueSet>

this results in the following error:Error from server: The filter "abstract = false" was not understood in the context of http://nucc.org/provider-taxonomy

IF is not the code is it a problem with the codesystem properties?

Grahame Grieve (Aug 04 2020 at 21:18):

is this in an IG where I can reproduce?

Eric Haas (Aug 04 2020 at 23:22):

US Core CI Build: https://build.fhir.org/ig/HL7/US-Core/ValueSet-us-core-provider-specialty.html

Michael Lawley (Aug 05 2020 at 00:05):

Since abstract is not a pre-defined property (see https://www.hl7.org/fhir/codesystem.html#status), it would need to be declared in the CodeSystem

Michael Lawley (Aug 05 2020 at 00:08):

But I don't even see properties on the codes in the CodeSystem that indicate abstractness in the http://nucc.org/provider-taxonomy CodeSystem, so I wouldn't expect this filter do be doing anything.

John Moehrke (Aug 05 2020 at 01:29):

note the newer IG publisher did work for me

Eric Haas (Aug 05 2020 at 14:23):

Is working for me as well

Grahame Grieve (Aug 06 2020 at 03:15):

yes I think it's resolved.

Last updated: Apr 12 2022 at 19:14 UTC