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Update ignore warnings (#387)
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* fix broken link in HistoryOfMetastatic, and replace all of mCODE links with the fsh-generated md links to avoid reduce future maintenance effort

* update ignore warnings

* added detailed FSN messages

* Update ignoreWarnings.txt

* Update ignoreWarnings.txt

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Co-authored-by: Mark Kramer <[email protected]>
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@saulakravitz @markkramerus
saulakravitz and markkramerus committed Sep 21, 2023
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Showing 1 changed file with 37 additions and 14 deletions.
51 changes: 37 additions & 14 deletions input/ignoreWarnings.txt
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Expand Up @@ -13,7 +13,6 @@ Error from server: Unable to provide support for code system https://ncicb.nci.ni
Error from server: Unable to provide support for code system https://terminology.hl7.org/CodeSystem/icd-o-3
Error from server: Unable to provide support for code system https://cancerstaging.org
Error from server: Unable to provide support for code system https://www.ama-assn.org/go/cpt
Error from server: Unable to provide support for code system https://hl7.org/fhir/us/mcode/CodeSystem/snomed-requested-cs
Error from server: HGVS is not supported at this time
Code System URI 'https://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl' is unknown so the code cannot be validated
Code System URI 'https://www.ncbi.nlm.nih.gov/gtr' is unknown so the code cannot be validated
Expand All @@ -29,7 +28,6 @@ The definition for the Code System with URI 'https://ncicb.nci.nih.gov/xml/owl/EV
The definition for the Code System with URI 'https://www.ncbi.nlm.nih.gov/clinvar' doesnt provide any codes so the code cannot be validated
Unknown System 'https://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl' specified, so Concepts and Filters can't be checked (Details: Resolved system https://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl (v3.0.0), but the definition is not complete)
Unable to check whether the code is in the value set https://hl7.org/fhir/us/mcode/ValueSet/mcode-cancer-stage-type-vs|3.0.0
Observation.code: Unable to check whether the code is in the value set https://hl7.org/fhir/us/mcode/ValueSet/mcode-cancer-stage-type-vs|3.0.0

# TG263 is a proprietary codesystem used in Radiotherapy. The whole point of conceptmaps is to make it easy to transition to the ValueSets used in this IG. The codesystem identifers TRX, IJE and MRE are not proper codesystem URIs. Work is underway to define proper URIs that will be included in future versions of this IG.
WARNING: ConceptMap/TG263CM: ConceptMap.group[0].source: The Source Code System TG263 is not fully defined and populated, and no sourceScope is specified, so the source code checking will not be performed
Expand All @@ -47,29 +45,54 @@ The valueSet reference https://loinc.org/vs/LL1040-6 on element Observation.compo
The valueSet reference https://loinc.org/vs/LL4986-7 on element Observation.interpretation could not be resolved

# SUPPRESS INFORMATION MESSAGES "DOES NOT MATCH ANY KNOWN SLICE" DUE TO TERMINOLOGY LIMITATIONS
This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
This element does not match any known slice defined in the profile https://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication|2.0.0
This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|3.0.0
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[1].resource/*DiagnosticReport/gx-genomics-report-adam-anyperson*/.result[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[1].resource/*DiagnosticReport/gx-genomics-report-adam-anyperson*/.result[6]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[1].resource/*DiagnosticReport/gx-genomics-report-adam-anyperson*/.result[7]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[1].resource/*DiagnosticReport/gx-genomics-report-adam-anyperson*/.result[13]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[1].resource/*DiagnosticReport/gx-genomics-report-adam-anyperson*/.result[14]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[14].resource/*Observation/gx-genomic-diagnostic-implication-bap1*/.derivedFrom[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication|2.0.0
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[15].resource/*Observation/gx-genomic-diagnostic-implication-pof1b*/.derivedFrom[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication|2.0.0
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[16].resource/*Observation/gx-genomic-diagnostic-implication-polrmt*/.derivedFrom[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication|2.0.0
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[27]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|3.0.0
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[30]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|3.0.0
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[38]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|3.0.0
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[39]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|3.0.0
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[8].resource/*DiagnosticReport/genomics-report-jenny-m*/.result[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: DiagnosticReport/genomics-report-jenny-m: DiagnosticReport.result[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: DiagnosticReport/genomics-report-john-anyperson: DiagnosticReport.result[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: DiagnosticReport/gx-genomics-report-adam-anyperson: DiagnosticReport.result[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: DiagnosticReport/gx-genomics-report-adam-anyperson: DiagnosticReport.result[6]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: DiagnosticReport/gx-genomics-report-adam-anyperson: DiagnosticReport.result[7]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: DiagnosticReport/gx-genomics-report-adam-anyperson: DiagnosticReport.result[13]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: DiagnosticReport/gx-genomics-report-adam-anyperson: DiagnosticReport.result[14]: This element does not match any known slice defined in the profile https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|3.0.0
INFORMATION: Observation/gx-genomic-diagnostic-implication-bap1: Observation.derivedFrom[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication|2.0.0
INFORMATION: Observation/gx-genomic-diagnostic-implication-pof1b: Observation.derivedFrom[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication|2.0.0
INFORMATION: Observation/gx-genomic-diagnostic-implication-polrmt: Observation.derivedFrom[0]: This element does not match any known slice defined in the profile https://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication|2.0.0


# DETAILS MESSAGES (THEY APPEAR TO BE FOR GROUPING PURPOSES ONLY)
Details for Observation/genomic-variant-jenny-m matching against profile https://hl7.org/fhir/StructureDefinition/Observation|4.0.1
Details for Observation/gx-genomic-variant-somatic-polrmt matching against profile https://hl7.org/fhir/StructureDefinition/Observation|4.0.1
Details for Observation/gx-genomic-variant-somatic-pof1b matching against profile https://hl7.org/fhir/StructureDefinition/Observation|4.0.1
Details for Observation/gx-genomic-variant-somatic-bap1-indel matching against profile https://hl7.org/fhir/StructureDefinition/Observation|4.0.1

# IG Publisher Bugs
This SNOMED-CT based include has some concepts with semantic tags (FSN terms) and some without (preferred terms) - check that this is what is intended
Rule dom-6: 'A resource should have narrative for robust management' Failed (defined in https://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)
# Suspected Bugs in IG Publisher -- Spurious warnings
WARNING: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[1].resource/*DiagnosticReport/gx-genomics-report-adam-anyperson*/: Rule dom-6: 'A resource should have narrative for robust management' Failed (defined in https://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)
WARNING: DiagnosticReport/gx-genomics-report-adam-anyperson: DiagnosticReport: Rule dom-6: 'A resource should have narrative for robust management' Failed (defined in https://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)


INFORMATION: ValueSet/mcode-cancer-stage-type-vs: ValueSet.compose.include[0]: This SNOMED-CT based include has some concepts with semantic tags (FSN terms) and some without (preferred terms) - check that this is what is intended
INFORMATION: ValueSet/mcode-radiotherapy-treatment-location-vs: ValueSet.compose.include[0]: This SNOMED-CT based include has some concepts with semantic tags (FSN terms) and some without (preferred terms) - check that this is what is intended

# UCUM Best Practice warning is inherited from Genomics Reporting IG
# UCUM Best Practice warning is inherited from Genomics Reporting IG and we can't change that
UCUM Codes that contain human readable annotations like {Base} can be misleading. Best Practice is not to use annotations in the UCUM code, and rather to make sure that Quantity.unit is correctly human readable

# Reference to deprecated extension included for backwards compatibility
The extension https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-treatment-termination-reason|3.0.0 is retired
StructureDefinition.where(url = 'https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-treatment-termination-reason'): The Implementation Guide contains no examples for this extension
# Reference to deprecated extension included for backwards compatibility.
INFORMATION: StructureDefinition/mcode-radiotherapy-course-summary: Procedure.extension: The extension https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-treatment-termination-reason|3.0.0 is retired
WARNING: StructureDefinition.where(url = 'https://hl7.org/fhir/us/mcode/StructureDefinition/mcode-treatment-termination-reason'): The Implementation Guide contains no examples for this extension

# Reference to condition-category code system is inherited from US Core
# Reference to condition-category code system is inherited from US Core and we can't change that
Reference to draft item https://terminology.hl7.org/CodeSystem/condition-category|0.5.0

# Big Value Set
# Too Big Value Set
The value set include has too many codes to validate (1,045)

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