Stream: conformance
Topic: validation issue
Rob Hausam (Jan 09 2020 at 07:45):
In trying to resolve the remaining errors in the IPS IG, I've run into this validation issue (attempting to isolate the problem by validating directly against an example instance using the specific profile (http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips):
RHausamMacbookPro:fhir-ips rhausam$ java -jar ~/Downloads/org.hl7.fhir.validator.jar -version 4.0.1 ~/Documents/Condition-example-ips.xml -ig hl7.fhir.uv.ips -profile http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips
FHIR Validation tool Version 4.1.41-SNAPSHOT (Git# bdab9a78b39a). Built 2019-12-31T14:32:35.701+11:00 (9 days old)
Detected Java version: 13.0.1 from /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home on x86_64 (64bit). 4096MB available
Arguments: -version 4.0.1 /Users/rhausam/Documents/Condition-example-ips.xml -ig hl7.fhir.uv.ips -profile http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips
Directories: Current = /Users/rhausam/git-repo/fhir-ips, Package Cache = /Users/rhausam/.fhir/packages
.. FHIR Version 4.0, definitions from hl7.fhir.r4.core#4.0.1
.. connect to tx server @ http://tx.fhir.org
(v4.0.1)
+ .. load IG from hl7.fhir.uv.ips
... Using version dev
.. validate [/Users/rhausam/Documents/Condition-example-ips.xml] against [http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips]
Terminology server: Check for supported code systems for http://loinc.org
*FAILURE* validating /Users/rhausam/Documents/Condition-example-ips.xml: error:1 warn:0 info:2
Error @ Condition.code.coding[0] (line 35, col17) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#198436008'
Information @ Condition.code (line 34, col11) : This element does not match any known slice for the profile http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips
Information @ Condition.code (line 34, col11) : None of the codes provided are in the value set http://hl7.org/fhir/uv/ips/ValueSet/core-problem-list-disorders-uv-ips (http://hl7.org/fhir/uv/ips/ValueSet/core-problem-list-disorders-uv-ips, and a code is recommended to come from this value set) (codes = http://snomed.info/sct#198436008)
This is the example instance:
<?xml version="1.0" encoding="utf-8"?>
<Condition xmlns="http://hl7.org/fhir" xmlns:xhtml="http://www.w3.org/1999/xhtml">
<id value="c64139e7-f02d-409c-bf34-75e8bf23bc80"/>
<identifier>
<system value="urn:oid:1.2.3.999"/>
<value value="c87bf51c-e53c-4bfe-b8b7-aa62bdd93002"/>
</identifier>
<clinicalStatus>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/condition-clinical"/>
<code value="active"/>
</coding>
</clinicalStatus>
<verificationStatus>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/condition-ver-status"/>
<code value="confirmed"/>
</coding>
</verificationStatus>
<category>
<coding>
<system value="http://loinc.org"/>
<code value="75326-9"/>
<display value="Problem"/>
</coding>
</category>
<severity>
<coding>
<system value="http://loinc.org"/>
<code value="LA6751-7"/>
<display value="Moderate"/>
</coding>
</severity>
<code>
<coding>
<system value="http://snomed.info/sct"/>
<code value="198436008"/>
<display value="Menopausal flushing (finding)">
<extension url="http://hl7.org/fhir/StructureDefinition/translation">
<extension url="lang">
<valueCode value="nl-NL"/>
</extension>
<extension url="content">
<valueString value="opvliegers"/>
</extension>
</extension>
</display>
</coding>
<!--
<coding>
<system value="http://hl7.org/fhir/sid/icd-10"/>
<code value="N95.1"/>
<display value="Menopausal and female climacteric states"/>
</coding>
-->
</code>
<subject>
<reference value="Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8"/>
</subject>
<onsetDateTime value="2015"/>
<recordedDate value="2016-10"/>
</Condition>
The validator appears to be assuming a "version" of '900000000000207008'? The code system version isn't specified in the value set definition or in the example instance, and '900000000000207008' isn't a valid edition module id and obviously isn't a valid SNOMED CT version url. The code '198436008' is a valid member of the value set. There is not a defined slice of 'Condition.code' that matches this example instance, but that's by design with open slicing and the binding to the core-problem-list-disorders-uv-ips value set in the base 'Condition.code' element. Unless I've missed something, it seems to me that this all should be able to validate correctly. @Grahame Grieve? @Lloyd McKenzie?
@Giorgio Cangioli
Rob Hausam (Jan 09 2020 at 20:30):
Any ideas on this - @Grahame Grieve? @Lloyd McKenzie?
Lloyd McKenzie (Jan 09 2020 at 20:46):
There are some similar issues about the SNOMED version not being looked at correctly. I'm deferring to @Grahame Grieve
Rob Hausam (Jan 09 2020 at 20:53):
Yes, we've had some issues with that. I thought they had been at least mostly resolved - but apparently not completely. If Grahame isn't able to get into it at the moment I can try to take a look at the code.
Grahame Grieve (Jan 13 2020 at 05:31):
is this still an issue? I can't reproduce it?
Rob Hausam (Jan 13 2020 at 16:08):
@Grahame Grieve Yes, it's still an issue with 4.1.42-SNAPSHOT. I'm getting the same error.
Grahame Grieve (Jan 13 2020 at 19:49):
have you cleared your txCache?
Rob Hausam (Jan 13 2020 at 21:06):
maybe not recently - I'll see what that does
Rob Hausam (Jan 14 2020 at 17:25):
@Grahame Grieve I cleared the txCache for the IPS IG, and that did help some. But unless I'm forgetting something, txCache isn't in play for the standalone validator which is where I'm seeing many of these issues (particularly "Unable to provide support for code system http://snomed.info/sct version 900000000000207008"). And I'm trying to work out why there is a noticeably different set of qa messages depending on whether I'm evaluating the example bundle instance while building the IG, or validating the bundle instance with the standalone validator against the IPS IG, or validating the individual resource instances (pulled out from the bundle) against the IG and the particular applicable profile - all three cases return a different set of messages for the same resource instance.
Grahame Grieve (Jan 14 2020 at 19:05):
well, what's an example with the validator directly?
Grahame Grieve (Jan 14 2020 at 19:05):
well, what's an example with the validator directly?
Grahame Grieve (Jan 14 2020 at 19:06):
well, what's an example with the validator directly?
Rob Hausam (Jan 14 2020 at 19:10):
I'll go ahead and post the examples
Rob Hausam (Jan 15 2020 at 06:33):
The is the example bundle instance. The IG build (1.0.40-SNAPSHOT) information messages (no warnings or errors) for the IPS-bundle-01.xml example bundle (with no suppressed qa messages) are:
== /Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml == INFORMATION: Bundle/IPS-examples-Bundle-01: Bundle.entry[4].resource.severity: None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-severity (http://hl7.org/fhir/ValueSet/condition-severity, and a code is recommended to come from this value set) (codes = http://loinc.org#LA6751-7) INFORMATION: Bundle/IPS-examples-Bundle-01: Bundle.entry[7].resource.code.coding[1]: Code System URI 'urn:oid:2.16.840.1.113883.2.4.4.1' is unknown so the code cannot be validated INFORMATION: Bundle/IPS-examples-Bundle-01: Bundle.entry[7].resource.code.coding[2]: Code System URI 'urn:oid:2.16.840.1.113883.2.4.4.7' is unknown so the code cannot be validated INFORMATION: Bundle/IPS-examples-Bundle-01: Bundle.entry[10].resource.severity: None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-severity (http://hl7.org/fhir/ValueSet/condition-severity, and a code is recommended to come from this value set) (codes = http://loinc.org#LA6750-9)
The validation results for the IPS-bundle-01.xml example bundle instance are:
RHausamMacbookPro:org.hl7.fhir.core rhausam$ java -jar ~/Downloads/org.hl7.fhir.validator.jar -version 4.0.1 ~/git-repo/fhir-ips/examples/IPS-bundle-01.xml -ig hl7.fhir.uv.ips
FHIR Validation tool Version 4.1.45-SNAPSHOT (Git# 9f1697dad160). Built 2020-01-15T08:08:25.901+11:00 (9 hours old)
Detected Java version: 13.0.1 from /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home on x86_64 (64bit). 4096MB available
Arguments: -version 4.0.1 /Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml -ig hl7.fhir.uv.ips
Directories: Current = /Users/rhausam/git-repo/org.hl7.fhir.core, Package Cache = /Users/rhausam/.fhir/packages
.. FHIR Version 4.0, definitions from hl7.fhir.r4.core#4.0.1
.. connect to tx server @ http://tx.fhir.org
(v4.0.1)
+ .. load IG from hl7.fhir.uv.ips
... Using version dev
.. validate [/Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml]
Terminology server: Check for supported code systems for http://loinc.org
*FAILURE* validating /Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml: error:14 warn:4 info:4
Error @ Bundle.entry[4].resource.code.coding[0] (line 441, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#198436008'
Error @ Bundle.entry[7].resource.code.coding[0] (line 561, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#108774000'
Error @ Bundle.entry[8].resource.code.coding[0] (line 592, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#412588001'
Error @ Bundle.entry[9].resource.code.coding[0] (line 642, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#373270004'
Error @ Bundle.entry[10].resource.code.coding[0] (line 692, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#254837009'
Error @ Bundle.entry[12].resource.value.ofType(CodeableConcept).coding[0] (line 762, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#278149003'
Error @ Bundle.entry[16].resource.hasMember[0].resource.value.ofType(CodeableConcept).coding[0] (line 762, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#278149003'
Error @ Bundle.entry[13].resource.value.ofType(CodeableConcept).coding[0] (line 796, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#10828004'
Error @ Bundle.entry[16].resource.hasMember[1].resource.value.ofType(CodeableConcept).coding[0] (line 796, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#10828004'
Error @ Bundle.entry[14].resource.value.ofType(CodeableConcept).coding[0] (line 830, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#10828004'
Error @ Bundle.entry[16].resource.hasMember[2].resource.value.ofType(CodeableConcept).coding[0] (line 830, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#10828004'
Error @ Bundle.entry[15].resource.value.ofType(CodeableConcept).coding[0] (line 864, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#260385009'
Error @ Bundle.entry[16].resource.hasMember[3].resource.value.ofType(CodeableConcept).coding[0] (line 864, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#260385009'
Error @ Bundle.entry[18].resource.value.ofType(CodeableConcept).coding[0] (line 978, col14) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#115329001'
Information @ Bundle.entry[4].resource.severity (line 433, col15) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-severity (http://hl7.org/fhir/ValueSet/condition-severity, and a code is recommended to come from this value set) (codes = http://loinc.org#LA6751-7)
Information @ Bundle.entry[10].resource.severity (line 684, col15) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-severity (http://hl7.org/fhir/ValueSet/condition-severity, and a code is recommended to come from this value set) (codes = http://loinc.org#LA6750-9)
Information @ Bundle.entry[7].resource.code.coding[1] (line 566, col14) : Code System URI 'urn:oid:2.16.840.1.113883.2.4.4.1' is unknown so the code cannot be validated
Information @ Bundle.entry[7].resource.code.coding[2] (line 571, col14) : Code System URI 'urn:oid:2.16.840.1.113883.2.4.4.7' is unknown so the code cannot be validated
Warning @ Bundle.entry[1].resource.contact[0].relationship[0] (line 322, col20) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/patient-contactrelationship (http://hl7.org/fhir/ValueSet/patient-contactrelationship, and a code should come from this value set unless it has no suitable code) (codes = http://terminology.hl7.org/CodeSystem/v3-RoleCode#MTH)
Warning @ Bundle.entry[4].resource.subject.resource.contact[0].relationship[0] (line 322, col20) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/patient-contactrelationship (http://hl7.org/fhir/ValueSet/patient-contactrelationship, and a code should come from this value set unless it has no suitable code) (codes = http://terminology.hl7.org/CodeSystem/v3-RoleCode#MTH)
Warning @ Bundle.entry[4].resource.category[0] (line 426, col15) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-category (http://hl7.org/fhir/ValueSet/condition-category, and a code should come from this value set unless it has no suitable code) (codes = http://loinc.org#75326-9)
Warning @ Bundle.entry[10].resource.category[0] (line 677, col15) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-category (http://hl7.org/fhir/ValueSet/condition-category, and a code should come from this value set unless it has no suitable code) (codes = http://loinc.org#75326-9)
Rob Hausam (Jan 15 2020 at 06:50):
This is the Condition resource instance ([4] in the bundle) extracted from the bundle. The validation results for the Condition resource instance are:
RHausamMacbookPro:org.hl7.fhir.core rhausam$ java -jar ~/Downloads/org.hl7.fhir.validator.jar -version 4.0.1 ~/Documents/Condition-example-ips.xml -ig hl7.fhir.uv.ips -profile http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips
FHIR Validation tool Version 4.1.45-SNAPSHOT (Git# 9f1697dad160). Built 2020-01-15T08:08:25.901+11:00 (9 hours old)
Detected Java version: 13.0.1 from /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home on x86_64 (64bit). 4096MB available
Arguments: -version 4.0.1 /Users/rhausam/Documents/Condition-example-ips.xml -ig hl7.fhir.uv.ips -profile http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips
Directories: Current = /Users/rhausam/git-repo/org.hl7.fhir.core, Package Cache = /Users/rhausam/.fhir/packages
.. FHIR Version 4.0, definitions from hl7.fhir.r4.core#4.0.1
.. connect to tx server @ http://tx.fhir.org
(v4.0.1)
+ .. load IG from hl7.fhir.uv.ips
... Using version dev
.. validate [/Users/rhausam/Documents/Condition-example-ips.xml] against [http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips]
Terminology server: Check for supported code systems for http://loinc.org
*FAILURE* validating /Users/rhausam/Documents/Condition-example-ips.xml: error:1 warn:0 info:2
Error @ Condition.code.coding[0] (line 35, col17) : Unable to provide support for code system http://snomed.info/sct version 900000000000207008 for 'http://snomed.info/sct#198436008'
Information @ Condition.code (line 34, col11) : This element does not match any known slice for the profile http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips
Information @ Condition.code (line 34, col11) : None of the codes provided are in the value set http://hl7.org/fhir/uv/ips/ValueSet/core-problem-list-disorders-uv-ips (http://hl7.org/fhir/uv/ips/ValueSet/core-problem-list-disorders-uv-ips, and a code is recommended to come from this value set) (codes = http://snomed.info/sct#198436008)
May Terry (Jan 17 2020 at 00:44):
I'm also getting the same Unable to provide support for code system http://snomed.info/sct version 900000000000207008 error that @Rob Hausam is reporting. I'm using FHIR Validation tool Version 4.1.47-SNAPSHOT
Grahame Grieve (Jan 17 2020 at 00:46):
ok how can I reproduce this?
Rob Hausam (Jan 17 2020 at 01:22):
I think I gave you information that should let you reproduce it in my post yesterday? I haven't tried 4.1 47 yes - I'll be able to get back and do that a bit later.
Grahame Grieve (Jan 17 2020 at 02:18):
ok sorted next release
Last updated: Apr 12 2022 at 19:14 UTC
