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Merge pull request #129 from onc-healthit/develop
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merge develop into master for 3.1.52 October 2021 SITE release
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@drbgfc
drbgfc authored Oct 26, 2021
2 parents 4d906fd + 0e11886 commit c90508c
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Showing 6 changed files with 705 additions and 7 deletions.
8 changes: 4 additions & 4 deletions pom.xml
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Expand Up @@ -3,7 +3,7 @@

<groupId>org.sitenv</groupId>
<artifactId>referenceccdavalidator</artifactId>
<version>1.0.60</version>
<version>1.0.61</version>
<packaging>war</packaging>
<name>Reference CCDA Validator</name>

Expand All @@ -15,9 +15,9 @@
<code.validator.version>latestVersion</code.validator.version>
<content.validator.version>latestVersion</content.validator.version>
<!-- MDHT properties -->
<mdht.models.version>3.0.0.20210924</mdht.models.version>
<ds4pcontent.version>${mdht.models.version}</ds4pcontent.version>
<mdht.plugins.version>3.0.0.202109230500</mdht.plugins.version>
<mdht.models.version>3.0.0.20211021</mdht.models.version>
<ds4pcontent.version>${mdht.models.version}</ds4pcontent.version>
<mdht.plugins.version>3.0.0.202110121523</mdht.plugins.version>
</properties>

<repositories>
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95 changes: 92 additions & 3 deletions src/test/java/org/sitenv/referenceccda/test/tests/RefCCDATest.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
package org.sitenv.referenceccda.test.tests;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.sitenv.referenceccda.test.other.ReferenceValidationLogger.printResults;
import static org.sitenv.vocabularies.test.other.ValidationLogger.println;
Expand All @@ -14,13 +16,19 @@
import java.util.Arrays;
import java.util.List;

import org.apache.commons.io.IOUtils;
import org.apache.log4j.BasicConfigurator;
import org.eclipse.mdht.uml.cda.ClinicalDocument;
import org.eclipse.mdht.uml.cda.Patient;
import org.eclipse.mdht.uml.cda.Person;
import org.eclipse.mdht.uml.cda.Subject;
import org.eclipse.mdht.uml.cda.SubjectPerson;
import org.eclipse.mdht.uml.cda.util.CDAUtil;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.sitenv.contentvalidator.service.ContentValidatorService;
import org.sitenv.referenceccda.controllers.ReferenceCCDAValidationController;
import org.sitenv.referenceccda.dto.ValidationResultsDto;
import org.sitenv.referenceccda.services.ReferenceCCDAValidationService;
import org.sitenv.referenceccda.test.other.ReferenceValidationLogger;
Expand Down Expand Up @@ -65,7 +73,7 @@ public class RefCCDATest extends ReferenceValidationTester implements Validation
SUB_SOCIAL_HISTORY_WITH_BIRTH_SEX_OBS_TEMPLATE_SITE_3094 = 15,
SUB_PROCEDURES_WITH_DEVICE_IDENTIFIER_OBSERVATION_SITE_3218 = 16,
SUB_PROCEDURES_WITH_DEVICE_IDENTIFIER_OBSERVATION_BAD_VALUE_ROOT_SITE_3218 = 17,
DS4P_REFRAIN_OBSERVATION = 18,IVL_REAL_EXAMPLE=19,IVL_REAL_EXAMPLE2=20,REFERRAL_NOTE=21,REFERRAL_NOTE2=22;
DS4P_REFRAIN_OBSERVATION = 18,IVL_REAL_EXAMPLE=19,IVL_REAL_EXAMPLE2=20,REFERRAL_NOTE=21,REFERRAL_NOTE2=22,SDTCTEST=23,CONSOLNOTEACTIVITY=24,MEDICATION_SECTION_CODE_INVALID=25;


// Feel free to add docs to the end but don't alter existing data
Expand Down Expand Up @@ -95,7 +103,13 @@ public class RefCCDATest extends ReferenceValidationTester implements Validation
RefCCDATest.class.getResource("/ivl_real_example.xml").toURI(),
RefCCDATest.class.getResource("/ivl_real_example2.xml").toURI(),
RefCCDATest.class.getResource("/ReferralNote.xml").toURI(),
RefCCDATest.class.getResource("/ReferralNote2.xml").toURI()
RefCCDATest.class.getResource("/ReferralNote2.xml").toURI(),
RefCCDATest.class.getResource("/SDTCExtensionsTest.xml").toURI(),
RefCCDATest.class.getResource("/ConsolNoteActivity.xml").toURI(),
RefCCDATest.class.getResource("/MedicationSectionCodeInvalid.xml").toURI()




};
} catch (URISyntaxException e) {
Expand Down Expand Up @@ -806,6 +820,81 @@ public void referralnoteindparticipantname_ExpectPassTest() {
failIfIssueIsInResults(results, ValidationResultType.CCDA_MDHT_CONFORMANCE_ERROR, "CONF:1198-31645");
}

/*
* SITE-3348 ETT GG, Errata CDA-2008, MDHT: "A plethora of b.1 issues that we think are invalid"
*/
@Test
public void noteActivity_expectfailtest() {
List<RefCCDAValidationResult> results = validateDocumentAndReturnResults(
convertCCDAFileToString(CCDA_FILES[CONSOLNOTEACTIVITY]), CCDATypes.NON_SPECIFIC_CCDAR2);
passIfIssueIsInResults(results, ValidationResultType.CCDA_MDHT_CONFORMANCE_WARN, "3250-16940, 3250-16941");
}

/*
* SITE-3346 Validators triggers false error for MedicationSectionCode
*/
@Test
public void test_MedicationSectionCodeInvalid() {
List<RefCCDAValidationResult> results = validateDocumentAndReturnResults(
convertCCDAFileToString(CCDA_FILES[MEDICATION_SECTION_CODE_INVALID]), CCDATypes.NON_SPECIFIC_CCDAR2);
results = getMDHTErrorsFromResults(results);
passIfIssueIsInResults(results, ValidationResultType.CCDA_MDHT_CONFORMANCE_ERROR, "15387");
// check that it is returned only once
int codeSectionCounter=0;
for (RefCCDAValidationResult result : results) {
if (result.getDescription() !=null && result.getDescription().contains("15387")) {
codeSectionCounter++;
}
}
assertTrue(codeSectionCounter==1);
}


/**
* parseSDTCExtensionsTest test for the ability to parse extensions
* Do not see much need to have negative tests
*
* @throws IOException
* @throws Exception
*/
@Test
public void parseSDTCExtensionsTest() throws IOException, Exception {
ClinicalDocument sdtcTestDocument = CDAUtil.load(IOUtils.toInputStream(convertCCDAFileToString(CCDA_FILES[SDTCTEST]), "UTF-8"));
assertNotNull("sdtcTestDocument.getSDTCStatusCode",sdtcTestDocument.getSDTCStatusCode());
assertEquals("sdtcTestDocument.getSDTCStatusCode","ClinicalDocumentStatusCode",sdtcTestDocument.getSDTCStatusCode().getCode());
Patient patient = sdtcTestDocument.getRecordTargets().get(0).getPatientRole().getPatient();
assertFalse("patient.getSDTCEthnicGroupCodes",patient.getSDTCEthnicGroupCodes().isEmpty());
assertEquals("patient.getSDTCEthnicGroupCodes","PatientEthnicGroupCode",patient.getSDTCEthnicGroupCodes().get(0).getCode());
assertFalse("patient.getSDTCRaceCodes",patient.getSDTCRaceCodes().isEmpty());
assertEquals("patient.getSDTCRaceCodes","PateintRaceCode",patient.getSDTCRaceCodes().get(0).getCode());
assertFalse( "patient.getSDTCDeceasedInd" , patient.getSDTCDeceasedInd().getValue() );
assertNotNull("patient.getSDTCDeceasedTime",patient.getSDTCDeceasedTime());
assertEquals("patient.getSDTCDeceasedTime","1900",patient.getSDTCDeceasedTime().getValue());
assertNotNull("patient.getSDTCDesc",patient.getSDTCDesc());
assertEquals("patient.getSDTCDesc","PatientDescription",patient.getSDTCDesc().getText());
assertTrue("patient.getSDTCMultipleBirthInd",patient.getSDTCMultipleBirthInd().getValue());
assertNotNull("patient.getSDTCMultipleBirthOrderNumber",patient.getSDTCMultipleBirthOrderNumber());
assertEquals("patient.getSDTCMultipleBirthOrderNumber","3",patient.getSDTCMultipleBirthOrderNumber().getValue().toString());
Person person = sdtcTestDocument.getAuthors().get(0).getAssignedAuthor().getAssignedPerson();
assertNotNull("person.getSDTCAsPatientRelationship",person.getSDTCAsPatientRelationship());
assertEquals("person.getSDTCAsPatientRelationship","AsPatientRelationship",person.getSDTCAsPatientRelationship().getText());
assertNotNull("person.getSDTCDesc",person.getSDTCDesc());
assertEquals("person.getSDTCDesc","PersonDescription",person.getSDTCDesc().getText());
SubjectPerson subjectPerson = sdtcTestDocument.getSections().get(0).getSubject().getRelatedSubject().getSubject();
assertFalse("subjectPerson.getSDTCEthnicGroupCodes",subjectPerson.getSDTCEthnicGroupCodes().isEmpty());
assertEquals("subjectPerson.getSDTCEthnicGroupCodes","SubjectEthnicGroupCode",subjectPerson.getSDTCEthnicGroupCodes().get(0).getCode());
assertFalse("subjectPerson.getSDTCRaceCodes",subjectPerson.getSDTCRaceCodes().isEmpty());
assertEquals("subjectPerson.getSDTCRaceCodes","SubjectRaceCode",subjectPerson.getSDTCRaceCodes().get(0).getCode());
assertTrue( "subjectPerson.getSDTCDeceasedInd" , subjectPerson.getSDTCDeceasedInd().getValue() );
assertNotNull("subjectPerson.getSDTCDeceasedTime",subjectPerson.getSDTCDeceasedTime());
assertEquals("subjectPerson.getSDTCDeceasedTime","1900",subjectPerson.getSDTCDeceasedTime().getValue());
assertNotNull("subjectPerson.getSDTCDesc",subjectPerson.getSDTCDesc());
assertEquals("subjectPerson.getSDTCDesc","SubjectDescription",subjectPerson.getSDTCDesc().getText());
assertTrue("subjectPerson.getSDTCMultipleBirthInd",subjectPerson.getSDTCMultipleBirthInd().getValue());
assertNotNull("subjectPerson.getSDTCMultipleBirthOrderNumber",subjectPerson.getSDTCMultipleBirthOrderNumber());
assertEquals("subjectPerson.getSDTCMultipleBirthOrderNumber","3",subjectPerson.getSDTCMultipleBirthOrderNumber().getValue().toString());
}


private static List<ConfiguredExpression> getGenericConfiguredExpressionsForTesting() {
final String validationMessage = "Will always fail";
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