Vocabulary Validation Setup issue

[Jason Countryman]

Good morning, all.

I've setup my in-house installation of the reference validator, and believe I am still having some setup issues that I can't identify.  Specifically with the vocabulary.

I'm testing my instance against the ETT instance using the negative testing CCDs.  My instance is not producing similar results.  For example, I expect to see:

Error - Code 106ABAC does not exist in the value set(s) 2.16.840.1.113762.1.4.1010.6

/ClinicalDocument[1]/comp onent[1]/structuredBody[1] /component[8]/section[1]/e ntry[1]/substanceAdministr ation[1]/consumable[1]/manufactu redProduct[1]/manufacturedMaterial[1]/code[1]

Line number: 1489

Actual Code: 106ABAC

Actual Display Name: TETANUS AND DIPHTHERIA TOXOIDS

When testing against the NT_CCDS_Sample4_r21_v3.xml file.  I am not getting that error in my instance.  

I do however get this, in the info:

ONC 2015 S&CC Vocabulary Validation Conformance Info

• Description: Value set code validation attempt for value set(s) ('2.16.840.1.113762.1.4.1010.6) that do not exist in service for code system CVX (2.16.840.1.113883.12.292)
• xPath: /ClinicalDocument[1]/component[1]/structuredBody[1]/component[8]/section[1]/entry[1]/substanceAdministration[1]/consumable[1]/manufacturedProduct[1]/manufacturedMaterial[1]/code[1]
• Document Line Number (approximate): 1489

Which leads me to believe that I am having a setup issue.  If there's any guidance anyone could provide, I would certainly appreciate it.  I can verify that the valuesets and codesystems seem to be loading correctly.  From the log file:

09:04:30,709 INFO  [VocabularyLoadRunner:92] Loading vocabularies at: /var/tomcat2/ValidatorConfig/CodeSystems...

09:04:30,709 INFO  [VocabularyLoadRunner:44] Loading files in : RXNORM...

09:05:24,626 INFO  [VocabularyLoadRunner:44] Loading files in : CDT...

09:05:25,822 INFO  [VocabularyLoadRunner:44] Loading files in : SNOMED-CT...

09:06:21,067 INFO  [VocabularyLoadRunner:44] Loading files in : CPT...

09:06:22,582 INFO  [VocabularyLoadRunner:44] Loading files in : ICD9CM_SG...

09:06:22,751 INFO  [VocabularyLoadRunner:44] Loading files in : ICD9CM_DX...

09:06:23,389 INFO  [VocabularyLoadRunner:44] Loading files in : ICD10CM...

09:06:35,318 INFO  [VocabularyLoadRunner:44] Loading files in : LOINC...

09:07:08,169 INFO  [VocabularyLoadRunner:44] Loading files in : ICD10PCS...

09:07:10,595 INFO  [VocabularyLoadRunner:94] Vocabularies loaded...

09:07:10,595 INFO  [VocabularyLoadRunner:99] Loading value sets at: /var/tomcat2/ValidatorConfig/ValueSets...

09:07:10,596 INFO  [VocabularyLoadRunner:44] Loading files in : VSAC...

09:07:10,596 INFO  [VsacLoader:34] Loading Value Set File: RelatedDocument.xlsx

09:07:10,688 INFO  [VsacLoader:34] Loading Value Set File: PlannedInterventionmoodCode.xlsx

09:07:10,723 INFO  [VsacLoader:34] Loading Value Set File: countryValueSet.xlsx

09:07:11,080 INFO  [VsacLoader:34] Loading Value Set File: RaceCategory.xlsx

09:07:11,109 INFO  [VsacLoader:34] Loading Value Set File: LanguageCode_RFC5646.xlsx

09:07:12,573 INFO  [VsacLoader:34] Loading Value Set File: WoundType.xlsx

09:07:12,593 INFO  [VsacLoader:34] Loading Value Set File: HealthcareAgentQualifier.xlsx

09:07:12,613 INFO  [VsacLoader:34] Loading Value Set File: PersonalAndLegalRelationshipRoleType.xlsx

09:07:12,645 INFO  [VsacLoader:34] Loading Value Set File: HealthcareServiceLocation.xlsx

09:07:12,680 INFO  [VsacLoader:34] Loading Value Set File: MoodeCodeEvnInt.xlsx

09:07:12,700 INFO  [VsacLoader:34] Loading Value Set File: SocialHistoryType.xlsx

09:07:12,721 INFO  [VsacLoader:34] Loading Value Set File: ProblemType.xlsx

09:07:12,740 INFO  [VsacLoader:34] Loading Value Set File: SurgicalOperationNoteDocumentTypeCode.xlsx

09:07:12,760 INFO  [VsacLoader:34] Loading Value Set File: PlannedmoodCodeObservation.xlsx

09:07:12,780 INFO  [VsacLoader:34] Loading Value Set File: ResidenceAndAccomodationType.xlsx

09:07:12,823 INFO  [VsacLoader:34] Loading Value Set File: CVXVaccinesAdminsteredVaccineSet_CDC.xlsx

09:07:12,856 INFO  [VsacLoader:34] Loading Value Set File: AdvanceDirectiveTypeCode.xlsx

09:07:12,876 INFO  [VsacLoader:34] Loading Value Set File: MedicationRouteFDA.xlsx

09:07:12,908 INFO  [VsacLoader:34] Loading Value Set File: ProblemStatus.xlsx

09:07:12,928 INFO  [VsacLoader:34] Loading Value Set File: HL7BasicConfidentialityKind.xlsx

09:07:12,946 INFO  [VsacLoader:34] Loading Value Set File: ParticipationFunction.xlsx

09:07:12,969 INFO  [VsacLoader:34] Loading Value Set File: PressurePoint.xlsx

09:07:12,987 INFO  [VsacLoader:34] Loading Value Set File: Race.xlsx

09:07:13,092 INFO  [VsacLoader:34] Loading Value Set File: BodySiteValueSet.xlsx

09:07:13,113 INFO  [VsacLoader:34] Loading Value Set File: NutritionalStatus.xlsx

09:07:13,133 INFO  [VsacLoader:34] Loading Value Set File: TransferDocumentType.xlsx

09:07:13,153 INFO  [VsacLoader:34] Loading Value Set File: HL7ReligiousAffiliation.xlsx

09:07:13,175 INFO  [VsacLoader:34] Loading Value Set File: CarePlan.xlsx

09:07:13,192 INFO  [VsacLoader:34] Loading Value Set File: ResultStatus.xlsx

09:07:13,206 INFO  [VsacLoader:34] Loading Value Set File: ClinicalDrugIngredient.xlsx

09:07:37,503 INFO  [VsacLoader:34] Loading Value Set File: HL7MaritalStatus.xlsx

09:07:37,518 INFO  [VsacLoader:34] Loading Value Set File: HL7LanguageAbilityMode.xlsx

09:07:37,532 INFO  [VsacLoader:34] Loading Value Set File: ObservationInterpretation.xlsx

09:07:37,548 INFO  [VsacLoader:34] Loading Value Set File: MedicationFillStatus.xlsx

09:07:37,564 INFO  [VsacLoader:34] Loading Value Set File: IngredientName.xlsx

09:07:44,042 INFO  [VsacLoader:34] Loading Value Set File: ProgressNoteDocumentTypeCode.xlsx

09:07:44,059 INFO  [VsacLoader:34] Loading Value Set File: MedicationDrugClass.xlsx

09:07:44,791 INFO  [VsacLoader:34] Loading Value Set File: HealthInsuranceType.xlsx

09:07:44,809 INFO  [VsacLoader:34] Loading Value Set File: DICOMPurposeOfReference.xlsx

09:07:44,828 INFO  [VsacLoader:34] Loading Value Set File: HealthcareProviderTaxonomyHIPAA.xlsx

09:07:44,892 INFO  [VsacLoader:34] Loading Value Set File: ActStatus.xlsx

09:07:44,907 INFO  [VsacLoader:34] Loading Value Set File: WoundMeasurements.xlsx

09:07:44,922 INFO  [VsacLoader:34] Loading Value Set File: MaritalStatus.xlsx

09:07:44,937 INFO  [VsacLoader:34] Loading Value Set File: ProblemSeverity.xlsx

09:07:44,953 INFO  [VsacLoader:34] Loading Value Set File: EntityNameUse.xlsx

09:07:44,968 INFO  [VsacLoader:34] Loading Value Set File: HPDocumentType.xlsx

09:07:44,985 INFO  [VsacLoader:34] Loading Value Set File: SmokingStatus.xlsx

09:07:45,001 INFO  [VsacLoader:34] Loading Value Set File: PlannedmoodCodeActEncounterProcedure.xlsx

09:07:45,015 INFO  [VsacLoader:34] Loading Value Set File: PatientEducation.xlsx

09:07:45,089 INFO  [VsacLoader:34] Loading Value Set File: PhysicalExamType.xlsx

09:07:45,106 INFO  [VsacLoader:34] Loading Value Set File: VaccineClinicalDrug.xlsx

09:07:45,140 INFO  [VsacLoader:34] Loading Value Set File: INDRoleclassCodes.xlsx

09:07:45,155 INFO  [VsacLoader:34] Loading Value Set File: DIRDocumentTypeCodes.xlsx

09:07:45,478 INFO  [VsacLoader:34] Loading Value Set File: HITSPVitalSignResultType.xlsx

09:07:45,493 INFO  [VsacLoader:34] Loading Value Set File: StateValueSet.xlsx

09:07:45,522 INFO  [VsacLoader:34] Loading Value Set File: DetailedEthnicity.xlsx

09:07:45,540 INFO  [VsacLoader:34] Loading Value Set File: Problem.xlsx

09:07:45,727 INFO  [VsacLoader:34] Loading Value Set File: CoverageRoleTypeValueSet.xlsx

09:07:45,741 INFO  [VsacLoader:34] Loading Value Set File: substanceintolerance.xlsx

09:07:53,245 INFO  [VsacLoader:34] Loading Value Set File: PriorityLevel.xlsx

09:07:53,258 INFO  [VsacLoader:34] Loading Value Set File: ActNoImmunizationReason.xlsx

09:07:53,271 INFO  [VsacLoader:34] Loading Value Set File: HealthStatus.xlsx

09:07:53,285 INFO  [VsacLoader:34] Loading Value Set File: PostalAddressUse.xlsx

09:07:53,300 INFO  [VsacLoader:34] Loading Value Set File: PostalCode.xlsx

09:07:55,661 INFO  [VsacLoader:34] Loading Value Set File: TobaccoUse.xlsx

09:07:55,680 INFO  [VsacLoader:34] Loading Value Set File: ProcedureNoteDocumentTypeCodes.xlsx

09:07:55,694 INFO  [VsacLoader:34] Loading Value Set File: ReferralDocumentType.xlsx

09:07:55,710 INFO  [VsacLoader:34] Loading Value Set File: UnitsOfMeasureCaseSensitive.xlsx

09:07:55,774 INFO  [VsacLoader:34] Loading Value Set File: FamilyMemberValue.xlsx

09:07:55,791 INFO  [VsacLoader:34] Loading Value Set File: FinanciallyResponsiblePartyTypeValueSet.xlsx

09:07:55,805 INFO  [VsacLoader:34] Loading Value Set File: SubstanceOtherThanClinicalDrug.xlsx

09:07:55,819 INFO  [VsacLoader:34] Loading Value Set File: MentalAndFunctionalStatusResponse.xlsx

09:07:55,832 INFO  [VsacLoader:34] Loading Value Set File: UB04PatientDischargeStatus.xlsx

09:07:55,850 INFO  [VsacLoader:34] Loading Value Set File: SensoryStatusProblemType.xlsx

09:07:55,862 INFO  [VsacLoader:34] Loading Value Set File: ActPriority.xlsx

09:07:55,875 INFO  [VsacLoader:34] Loading Value Set File: DischargeSummaryDocumentTypeCode.xlsx

09:07:55,887 INFO  [VsacLoader:34] Loading Value Set File: EntityPersonNamePartQualifier.xlsx

09:07:55,899 INFO  [VsacLoader:34] Loading Value Set File: AllergyAdverseEventType.xlsx

09:07:55,911 INFO  [VsacLoader:34] Loading Value Set File: ADLResultType.xlsx

09:07:55,923 INFO  [VsacLoader:34] Loading Value Set File: CriticalityObservation.xlsx

09:07:55,935 INFO  [VsacLoader:34] Loading Value Set File: ProblemActStatusCode.xlsx

09:07:55,946 INFO  [VsacLoader:34] Loading Value Set File: SupportedFileFormats.xlsx

09:07:55,959 INFO  [VsacLoader:34] Loading Value Set File: LanguageAbilityProficiency.xlsx

09:07:55,970 INFO  [VsacLoader:34] Loading Value Set File: DIRSectionTypeCodes.xlsx

09:07:55,983 INFO  [VsacLoader:34] Loading Value Set File: FullPHINVADSClinicalDrugName.xlsx

09:07:57,902 INFO  [VsacLoader:34] Loading Value Set File: EncounterPlanned.xlsx

09:07:57,924 INFO  [VsacLoader:34] Loading Value Set File: Payer.xlsx

09:07:57,947 INFO  [VsacLoader:34] Loading Value Set File: AdministrationUnitDoseForm.xlsx

09:07:57,960 INFO  [VsacLoader:34] Loading Value Set File: 2.16.840.1.113762.1.4.1010.6.xlsx

09:07:57,985 INFO  [VsacLoader:34] Loading Value Set File: MedicationProductFormValueSet.xlsx

09:07:58,007 INFO  [VsacLoader:34] Loading Value Set File: GoalAchievement.xlsx

09:07:58,019 INFO  [VsacLoader:34] Loading Value Set File: NutritionRecommendations.xlsx

09:07:58,031 INFO  [VsacLoader:34] Loading Value Set File: AdministrativeGenderHL7V3.xlsx

09:07:58,042 INFO  [VsacLoader:34] Loading Value Set File: Ability.xlsx

09:07:58,054 INFO  [VsacLoader:34] Loading Value Set File: PlannedmoodCodeSubstanceAdministrationSupply.xlsx

09:07:58,065 INFO  [VsacLoader:34] Loading Value Set File: TelecomUse.xlsx

09:07:58,076 INFO  [VsacLoader:34] Loading Value Set File: x_ServiceEventPerformer.xlsx

09:07:58,087 INFO  [VsacLoader:34] Loading Value Set File: ReferralTypes.xlsx

09:07:58,151 INFO  [VsacLoader:34] Loading Value Set File: Ethnicity.xlsx

09:07:58,164 INFO  [VsacLoader:34] Loading Value Set File: LanguageAbilityMode.xlsx

09:07:58,175 INFO  [VsacLoader:34] Loading Value Set File: VitalSignResults.xlsx

09:07:58,187 INFO  [VsacLoader:34] Loading Value Set File: ProcedureActStatusCode.xlsx

09:07:58,198 INFO  [VsacLoader:34] Loading Value Set File: UniqueIngredientIdentifier(UNII).xlsx

09:08:03,020 INFO  [VsacLoader:34] Loading Value Set File: TargetSiteQualifiers.xlsx

09:08:03,033 INFO  [VsacLoader:34] Loading Value Set File: MedicationClinicalDrug.xlsx

09:08:03,654 INFO  [VsacLoader:34] Loading Value Set File: PatientReferralActmoodCode.xlsx

09:08:03,667 INFO  [VsacLoader:34] Loading Value Set File: PressureUlcerStage.xlsx

09:08:03,678 INFO  [VsacLoader:34] Loading Value Set File: HITSPProblemStatus.xlsx

09:08:03,690 INFO  [VsacLoader:34] Loading Value Set File: EncounterTypeCode.xlsx

09:08:03,713 INFO  [VsacLoader:34] Loading Value Set File: ReligiousAffiliation.xlsx

09:08:03,729 INFO  [VsacLoader:34] Loading Value Set File: DIRQuantityMeasurementTypeCodes.xlsx

09:08:03,742 INFO  [VsacLoader:34] Loading Value Set File: AgePQ_UCUM.xlsx

09:08:03,754 INFO  [VsacLoader:34] Loading Value Set File: WoundCharacteristic.xlsx

09:08:03,767 INFO  [VsacLoader:34] Loading Value Set File: ConsultDocumentType.xlsx

09:08:03,782 INFO  [VocabularyLoadRunner:101] Value Sets loaded...

09:08:03,783 INFO  [VocabularyLoadRunner:105] !!!!*********** VOCABULARY DATABASE HAS FINISHED LOADING - SERVER WILL CONTINUE AND SHOULD BE DONE SHORTLY. ***********!!!!

Thanks,

Jason

[Jason Countryman]

Has anyone had anything similar to this?  I've been through all the instructions multiple times and can't find what I'm doing wrong.  I've upped the log level and haven't gotten any help that way either.  Just hoping for a place to start looking.

[Mike Burns]

I've been having this same issue.

On a whim I copied the data out of the VSAC file I downloaded and placed all the content into the ValueSet_format_Template.xls file, did a "Save As" to convert to xlsx, replaced the VSAC file on my sever with this new one and my valueset started to validate properly.

I'm thinking that maybe the format of the VSAC download file might have changed in a way that prevents the valuesets from loading properly.

I was about to open a new post about it when I searched and found this one.

[Jason Countryman]

Hmmm, that could be what I'm experiencing.  When the switch from xls to xlsx happened, I downloaded all new valuesets from vsac.  Thanks for the input.

[Mayank Pant]

Hi Mike,

Did you placed all the different valuesets that are downloaded from VSAC into one ValueSet_format_Template.xls file and did a "Save As" ?

And kept your ValueSet_format_Template.xls file inside ..\valueset_repository\VSAC. ?

Thanks !

[Mayank Pant]

Hi Mike,

Did you placed all the different valuesets that are downloaded from VSAC into one ValueSet_format_Template.xls file and did a "Save As" ?

And kept your ValueSet_format_Template.xls file inside ..\valueset_repository\VSAC. ?

If you can post me a screen print of your directory that will be more helpful !

Thanks !

On Wednesday, August 2, 2017 at 10:57:53 AM UTC+5:30, Mike Burns wrote:

[Mike Burns]

I didn't try all of the valuesets, I only did one.  (MedicationClinicalDrug).

But yes, I copied all the data from MedicationClinicalDrug.xlsx into the ValueSet_format_Templat.xls file.

Then did "Save As" MedicationClinicalDrugFromTemplate.xlsx.  

Replaced the MedicationClinicalDrug.xlsx file with MedicationClinicalDrugFromTemplate.xlsx in  .../vocabulary/valueset_repository/VSAC

Restarted the app sever.

When the application started, it loaded the new file.

1:29:29,384 INFO  [VocabularyLoadRunner:94] Vocabularies loaded...

21:29:29,385 INFO  [VocabularyLoadRunner:99] Loading value sets at: /usr/share/tomcat/ccda/vocabulary/valueset_repository...

21:29:29,386 INFO  [VocabularyLoadRunner:44] Loading files in : VSAC...

21:29:29,386 INFO  [VsacLoader:34] Loading Value Set File: Ethnicity.xlsx

21:29:29,478 INFO  [VsacLoader:34] Loading Value Set File: HL7LanguageAbilityMode.xlsx

...

21:29:34,609 INFO  [VsacLoader:34] Loading Value Set File: MedicationClinicalDrugFromTemplate.xlsx

...

and when I was done the only valueset that successfully validates is the one from my MedicationClinicalDrugFromTemplate.xlsx file.

I don't have time right now to dig in and see what the difference is that is causing the valueset to skip loading, but I bet it is because the valueset oid moved from row 3 to row 4 .

Old rows: (in template.xlsx file)

  Row 1  image

  Row 2  Value set name

  Row 3  OID

  Row 4 Type

  Row 5 Version

  Row 6  Steward

New rows: (VSAC download format)

  Row 1 image

  Row 2 Value Set Name

  Row 3  Code System (New Row)

  Row 4  OID

  Row 5  Type

  Row 6 Version

  Row 7  steward

I bet the code is stuffing the new "Code System" value into what it thinks is an OID.

[Mike Burns]

I just opened a ticket on the code-validator-api page:  https://github.com/siteadmin/code-validator-api/issues/47

They were using the row to calculate OID/type/etc, and those values are all off by one now. that Code System was inserted.

[Jason Countryman]

That would be it for me too, it looks like.  Great catch.

[Jason Countryman]

I looked into the source code, and in VsacLoader.java, it is definitely expecting the OID in row 3.  Consequently, it won't be picking up the Type, Version, or Steward correctly either.

I've fixed it in my copy of the code, in the codevalidator-api project.  Does anyone know how to create the referececcdaservice.war in eclipse neon?  I've not built this project before, just browsed the code.

[Jason Countryman]

Ok, I deleted the previous macro, as it only caught the first sheet.

Here's the one that gets both sheets.

Sub deleterow()

Dim Filename, Pathname, saveFileName As String

Dim wb As Workbook

Dim initialDisplayAlerts As Boolean

Dim pattern As String

pattern = "Code System"

Pathname = "C:\Users\jasonc\Documents\valuesetfilestoconvert\"  ' Needs to have a trailing \

Filename = Dir(Pathname & "*.xlsx")

initialDisplayAlerts = Application.DisplayAlerts

Application.DisplayAlerts = False

Do While Filename <> ""

    Set wb = Workbooks.Open(Filename:=Pathname & Filename, _

                            UpdateLinks:=False, ReadOnly:=False, Editable:=True)

    wb.CheckCompatibility = False

    

    

    

    If ActiveSheet.Cells(3, "A") = pattern Then

      ActiveSheet.Cells(3, "A").EntireRow.Delete

    End If

    

    Dim ws As Worksheet, wsCollection As Sheets

    

    Set wsCollection = Sheets

    Set ws = wb.Sheets("Code List")

    

    If ws.Cells(3, "A") = pattern Then

      ws.Cells(3, "A").EntireRow.Delete

    End If

    

    wb.Save

    wb.Close SaveChanges:=True

    Filename = Dir()

Loop

Application.DisplayAlerts = initialDisplayAlerts

End Sub

[Mayank Pant]

Hey Jason

Hope you are doing great !
Just wanted to know, are you able to generate the .war with the fixes(given above) you made in your local install?

Thank you for help !

[Jason Countryman]

Nope.  I wrote that excel macro to take out the row that VSAC added to the xlsx files.  It's a hacky fix, but it works for now.

[Mayank Pant]

Thank you Jason.
This works for me!
Now i m able to get some vocabulary valudation.
Although the errors are not equal in number as compared to the validator hosted by ETT.
I m going to check the valuesets(few non VSAC) now, for which there is a mismatch.

[Jason Countryman]

Glad I could help you out.  Remember though, if they fix the bug, these valuesets you have won't work anymore.

I'm having one lingering issue, I'm hoping someone else has seen and can point me in a direction.  I'm getting these results in the vocabulary info:

• ONC 2015 S&CC Vocabulary Validation Conformance Info

• • Description: Value set code validation attempt for value set(s) ('2.16.840.1.113883.1.11.12839) that do not exist in service for code system null (null)
  • xPath: /ClinicalDocument[1]/component[1]/structuredBody[1]/component[9]/section[1]/entry[1]/organizer[1]/component[2]/observation[1]/value[1]
  • Document Line Number (approximate): 1630

Just for that valueset though.  Its the UCUM valueset.  I've checked my .xlsx for that one and it appears to be correct.  I'm expecting to get errors for the valueset similar to:

      Error - Unit 'XYZZZZZZZ' does not exist in the value set (2.16.840.1.113883.1.11.12839)

         /ClinicalDocument[1]/comp onent[1]/structuredBody[1] /component[9]/section[1]/e ntry[1]/organizer[1]/component[1]/observation[1]/value[1]

         Line number: 1617

But I'm not getting them.  Anyone overcome an issue like this?

[Nagesh Bashyam]

We are looking into adding a fix that works with both formats…for the next release..

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[Mike Burns]

+100 for the macro.

Thanks Jason!

[Mayank Pant]

Good morning Dragon.Thanks for providing the info.
Can you please help us when are you planning for the next release?
This will help me in updating our team on the same.

Thanks !

[Jason Countryman]

Glad I could help.  Now if I could just figure out this UCUM issue I'm having, I'd be all set.

[Nagesh Bashyam]

The C-CDA validator releases are on the last Monday of every month.

The upcoming releases can be seen at : https://ttpedge.sitenv.org/ttp/#/edge/announcement

-----Original Message-----
From: edge-te...@googlegroups.com [mailto:edge-te...@googlegroups.com] On Behalf Of Mayank Pant
Sent: Thursday, August 10, 2017 1:34 AM
To: Edge Test Tool (ETT)

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[Mike Burns]

Hey Jason.

ONC 2015 S&CC Vocabulary Validation Conformance Info

• Description: Value set code validation attempt for value set(s) ('2.16.840.1.113883.1.11.12839) that do not exist in service for code system null (null)

That is the exact error I got when the value sets were not loading properly because of the headers out of order.

If I were you I would try recreating the valueset again.  

• I just tested again, and by copying the valueset into the valueSet_format_template,
• modifying the oid on both sheets
• inserting all the codes/values...
• manually add "/min"
• Not sure about the history here... the implementation guid has a list of recommended common types for vital signs, which includes "/min", but "/min" isn't in any copy of the valueset that I could find.
• Save as type .xlsx
• and place inside the VSAC directory.

After that, I modified a CCDA that I had with your bad code for a vital sign... XYZZZZ and got the following error:

ONC 2015 S&CC Vocabulary Validation Conformance Error

• Description: Unit 'XYZZZZZZZ' does not exist in the value set (2.16.840.1.113883.1.11.12839)
• xPath: /ClinicalDocument[1]/component[1]/structuredBody[1]/component[5]/section[1]/entry[2]/organizer[1]/component[2]/observation[1]/value[1]
• Document Line Number (approximate): 887

So I'm pretty sure that your .xlsx file for UnitsOfMeasure is just munged.

[Mayank Pant]

Hi Jason,
GoodMorning !
How are you doing ?

I just need to confirm an issue i m facing right now, I m unable to get vocab validation  errors for few of the valuesets, tomcat logs confirms error on loading these valuesets.

1. 2.16.840.1.113883.1.11.12839(ucum)
2. 2.16.840.1.113762.1.4.10100.1(Substance reactant for intolerence) - for this i m trying to merge the valuesets provided in the valuesets_instructions.docx and pasting in the template.*
 
i checked the value sets files seems fine like other valuesets.

Not sure what i m missing doing exactly.
 

Regards,
Mayank

[Jason Countryman]

Hmmm, I'm not sure how much help I can be.  I had issues with both of those valuesets, but they were both my mistakes once I got past the extra row issue.  The ucum in particular was a pain, as both the excel and word files for that are laid out just awfully by LOINC.

[Mayank Pant]

Jason , can u pls help me with loading the files that i m attaching in your vsac directory. I compared the same not sure where i m missing.

[Jason Countryman]

Your code system OID in the UCUM file is wrong.  Not the header one, but the data elements.  I'd check that for the other two files too.

[Mayank Pant]

Great..Thanks ! I followed the same ...and I m able to load the value set.I ll also go for the same for other two.

[Mayank Pant]

Hey Jason,

Can you please attach your files for the mentioned oid above. I m unable to figure out the issue.

I m waiting for the .war today which is supposed to be available in today's release.

[Jason Countryman]

Due to the licensing issues, I can't share my versions of the files.  Good luck.

[Mayank Pant]

oh okay. I have downloaded all the codes as mentioned in the Valusets_instruction.docx .

Anyways we are suppose to get a new released version of ccda ref validator today.  I m going to try that post that today.

[Mayank Pant]

Good morning Jason.

hope you are doing fine.

I tried with the latest release and tried with originak VSAC files. But for few of the files i need to remove the extra line from the VSAC file.
Are you facing the same issue?

[Jason Countryman]

I'm still using the valueset files from before the latest release.  The ones I removed the extra line from.  The release works just fine with them.

[Nagesh Bashyam]

The latest release should work with both formats based on what we know.

 

From: edge-te...@googlegroups.com [mailto:edge-te...@googlegroups.com] On Behalf Of Mayank Pant

Sent: Friday, September 01, 2017 8:18 AM
To: Edge Test Tool (ETT)

Subject: Re: Vocabulary Validation Setup issue

 

Good morning Jason.

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[Mayank Pant]

Hi Dragon,
Its not about the format. Its about the excel file having extra row of code system in the vsac file. After removing that only we are able to get vocab validation errors.This was a hack provided by Jason and Mike.
But when i use the original vsac file with latest release the issue persists.

Jason can you pls add if i miss anything?

[Mark McDougald]

Hey Mike, what directory did you put the valueSet_format_template file?  And, did you fill in every column, or just the Code|Code System|CodeSystem OID|TTY fields?

[Mark McDougald]

Jason, can you can you elaborate on ho wyou changed / added these valuesets?  

Also, where did you put this new file?  In the VSAC directory?

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[Jason Countryman]

Well, the changes I made to the valuesets are moot now, as the validator can handle both the previous vsac nlm format and the newer one.  All my valuesets are in the VSAC directory.

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[Mike Burns]

On Tuesday, November 7, 2017 at 8:26:43 PM UTC-6, Mark McDougald wrote:

Hey Mike, what directory did you put the valueSet_format_template file?  And, did you fill in every column, or just the Code|Code System|CodeSystem OID|TTY fields?

I only filled in the Code/Code System/OID at the top of the file. 

the valueSet_format_template needs to get renamed, and placed in your  VSAC directory.

In my case I placed all of the validator code right in the tomcat directory...  /usr/share/tomcat/ccda

so the final destination for the codeset from the template was

/usr/share/tomcat/ccda/vocabulary/valueset_repository/VSAC/<valuesetname>.xlsx

Here is a copy of my referenceccdaservice.xml

~tomcat/conf/Catalina/localhost/referenceccdaservice.xml

<Context reloadable="true">

    <Parameter name="vocabulary.localCodeRepositoryDir" value="/usr/share/tomcat/ccda/vocabulary/code_repository" override="true"/>

    <Parameter name="vocabulary.localValueSetRepositoryDir" value="/usr/share/tomcat/ccda/vocabulary/valueset_repository" override="true"/>

    <Parameter name="referenceccda.configFile" value="/usr/share/tomcat/ccda/ccdaReferenceValidatorConfig.xml" override="true"/>

    <Parameter name="content.scenariosDir" value="/usr/share/tomcat/ccda/scenarios" override="true"/>

</Context>

Notice that the endpoints for the code and repository dir are different than the ones in the instructions. The ones in the instructions were wrong.

And here is the snippet from directory structure under /usr/share/tomcat/ccda...

├── ccdaReferenceValidatorConfig.xml

├── scenarios

└── vocabulary

    ├── code_repository

    │   ├── ICD10CM

    │   │   └── icd10cm_order_2015.txt

    │   ├── ICD10PCS

    │   │   └── icd10pcs_order_2015.txt

    │   ├── ICD9CM_DX

    │   │   ├── CMS32_DESC_LONG_DX.txt

    │   │   └── CMS32_DESC_SHORT_DX.txt

    │   ├── LOINC

    │   │   └── loinc.csv

    │   ├── RXNORM

    │   │   └── RXNCONSO.RRF

    │   └── SNOMED-CT

    │       └── sct2_Description_Full-en_US1000124_20150901.txt

    ├── valueset_repository

    │   └── VSAC

    │       ├── Ability.xlsx

    │       ├── ActNoImmunizationReason.xlsx

    │       ├── ActPriority.xlsx

    │       ├── ADLResultType.xlsx

    │       ├── AdministrationUnitDoseForm.xlsx

    │       ├── AdministrativeGenderHL7V3.xlsx

    │       ├── AdvanceDirectiveTypeCode.xlsx

    │       ├── AllergyAdverseEventType.xlsx

...

[adam....@procentive.com]

"Notice that the endpoints for the code and repository dir are different than the ones in the instructions. The ones in the instructions were wrong." == Waaa??   Man oh man, why?

Thanks for your post.  Once I changed :

<Parameter name="vocabulary.localValueSetRepositoryDir" value="C:\ccdavalidator\vocabulary\valueset_repository\VSAC" override="true"/>

 to 

<Parameter name="vocabulary.localValueSetRepositoryDir" value="C:\ccdavalidator\vocabulary\valueset_repository" override="true"/>

in the referenceccdaservice.xml file I was able to actually load my first valueset.   (removed \VSAC)

Why has that not been corrected in the readme?

Also, does anyone know where to get all of the *.xlsx files that are supposed to go in the VSAC directory?   Or is everyone here manually creating ~90 .xlsx files?  (seems like that should be shared to save everyone from having to do this manually)

[Krishna Desai]

https://vsac.nlm.nih.gov/valueset/expansions?pr=all

1. Login
2. Click the check-box in the top-right
3. Click "Download" at the bottom
4. All files will be downloaded individually as a ZIP