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return codeableConcept from validate-code

This commit is contained in:
Grahame Grieve 2023-05-08 13:30:04 -05:00
parent 491b5ccb4a
commit ce46eee731
5 changed files with 43 additions and 8 deletions
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13
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
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@ -122,6 +122,7 @@ public interface IWorkerContext {
private String txLink;
private String diagnostics;
private List<OperationOutcomeIssueComponent> issues = new ArrayList<>();
private CodeableConcept codeableConcept;
@Override
public String toString() {
@ -276,7 +277,17 @@ public interface IWorkerContext {
public List<OperationOutcomeIssueComponent> getIssues() {
return issues;
}
public ValidationResult addCodeableConcept(CodeableConcept vcc) {
if (!vcc.isEmpty()) {
codeableConcept = vcc;
}
return this;
}
public CodeableConcept getCodeableConcept() {
return codeableConcept;
}
}

7
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeableConcept.java
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@ -408,6 +408,13 @@ public boolean hasCoding(String system, String code) {
@Override
public String toString() {
return hasCoding() ? getCoding().toString() : "["+getText()+"]";
}
public void removeCoding(String system, String version, String code) {
getCoding().removeIf(c ->
(system == null || system.equals(c.getSystem())) &&
(version == null || version.equals(c.getVersion())) &&
(code == null || code.equals(c.getCode())));
}
// end addition

24
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/validation/ValueSetValidator.java
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@ -158,6 +158,7 @@ public class ValueSetValidator {
// first, we validate the codings themselves
ValidationProcessInfo info = new ValidationProcessInfo();
CodeableConcept vcc = new CodeableConcept();
if (options.getValueSetMode() != ValueSetMode.CHECK_MEMERSHIP_ONLY) {
int i = 0;
for (Coding c : code.getCoding()) {
@ -183,7 +184,7 @@ public class ValueSetValidator {
}
} else {
c.setUserData("cs", cs);
res = validateCode(path+".coding["+i+"]", c, cs);
res = validateCode(path+".coding["+i+"]", c, cs, vcc);
}
info.getIssues().addAll(res.getIssues());
i++;
@ -202,6 +203,12 @@ public class ValueSetValidator {
} else if (ok) {
result = true;
foundCoding = c;
if (options.getValueSetMode() == ValueSetMode.CHECK_MEMERSHIP_ONLY) {
vcc.addCoding().setSystem(c.getSystem()).setVersion(c.getVersion()).setCode(c.getCode());
}
}
if (ok == null || !ok) {
vcc.removeCoding(c.getSystem(), c.getVersion(), c.getCode());
}
}
if (result == null) {
@ -222,6 +229,7 @@ public class ValueSetValidator {
res.setVersion(foundCoding.hasVersion() ? foundCoding.getVersion() : ((CodeSystem) foundCoding.getUserData("cs")).getVersion());
res.setDisplay(cd.getDisplay());
}
res.addCodeableConcept(vcc);
return res;
} else if (foundCoding == null) {
return new ValidationResult(IssueSeverity.ERROR, "Internal Error that should not happen", makeIssue(IssueSeverity.FATAL, IssueType.EXCEPTION, path, "Internal Error that should not happen"));
@ -229,11 +237,11 @@ public class ValueSetValidator {
String disp = lookupDisplay(foundCoding);
ConceptDefinitionComponent cd = new ConceptDefinitionComponent(foundCoding.getCode());
cd.setDisplay(disp);
return new ValidationResult(IssueSeverity.WARNING, info.summary(), foundCoding.getSystem(), getVersion(foundCoding), cd, disp, info.getIssues());
return new ValidationResult(IssueSeverity.WARNING, info.summary(), foundCoding.getSystem(), getVersion(foundCoding), cd, disp, info.getIssues()).addCodeableConcept(vcc);
} else {
ConceptDefinitionComponent cd = new ConceptDefinitionComponent(foundCoding.getCode());
cd.setDisplay(lookupDisplay(foundCoding));
return new ValidationResult(foundCoding.getSystem(), getVersion(foundCoding), cd, getPreferredDisplay(cd, null));
return new ValidationResult(foundCoding.getSystem(), getVersion(foundCoding), cd, getPreferredDisplay(cd, null)).addCodeableConcept(vcc);
}
}
@ -406,7 +414,7 @@ public class ValueSetValidator {
// we can't validate that here.
throw new FHIRException("Unable to evaluate based on empty code system");
}
res = validateCode(path, code, cs);
res = validateCode(path, code, cs, null);
} else if (cs == null && valueset.hasExpansion() && inExpansion) {
// we just take the value set as face value then
res = new ValidationResult(system, wv, new ConceptDefinitionComponent().setCode(code.getCode()).setDisplay(code.getDisplay()), code.getDisplay());
@ -589,7 +597,7 @@ public class ValueSetValidator {
return false;
}
private ValidationResult validateCode(String path, Coding code, CodeSystem cs) {
private ValidationResult validateCode(String path, Coding code, CodeSystem cs, CodeableConcept vcc) {
ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode());
if (cc == null) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
@ -600,8 +608,12 @@ public class ValueSetValidator {
return new ValidationResult(IssueSeverity.ERROR, msg, makeIssue(IssueSeverity.ERROR, IssueType.INVALID, path+".code", msg));
}
}
Coding vc = new Coding().setCode(code.getCode()).setSystem(cs.getUrl()).setVersion(cs.getVersion()).setDisplay(getPreferredDisplay(cc, cs));
if (vcc != null) {
vcc.addCoding(vc);
}
if (code.getDisplay() == null) {
return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs));
return new ValidationResult(code.getSystem(), cs.getVersion(), cc, vc.getDisplay());
}
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
if (cc.hasDisplay() && isOkLanguage(cs.getLanguage())) {

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/terminology/tests/ExternalTerminologyServiceTests.java
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@ -49,8 +49,10 @@ public class ExternalTerminologyServiceTests implements ITxTesterLoader {
}
private static final String SERVER = FhirSettings.getTxFhirDevelopment();
// private static final String SERVER = FhirSettings.getTxFhirLocal();
// private static final String SERVER = FhirSettings.getTxFhirLocal();
// private static final String SERVER = "https://r4.ontoserver.csiro.au/fhir";
@Parameters(name = "{index}: id {0}")
public static Iterable<Object[]> data() throws IOException {

3
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/terminology/tests/TerminologyServiceTests.java
View File

@ -274,6 +274,9 @@ public class TerminologyServiceTests {
if (vm.getDisplay() != null) {
res.addParameter("display", vm.getDisplay());
}
if (vm.getCodeableConcept() != null) {
res.addParameter("codeableConcept", vm.getCodeableConcept());
}
if (vm.getIssues().size() > 0) {
OperationOutcome oo = new OperationOutcome();
oo.getIssue().addAll(vm.getIssues());