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add value set qa checking

This commit is contained in:
Grahame Grieve 2023-07-21 21:17:12 +10:00
parent e324047735
commit 8980df2364
3 changed files with 93 additions and 6 deletions
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2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
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@ -922,6 +922,8 @@ public class I18nConstants {
public static final String TERMINOLOGY_TX_HINT = "TERMINOLOGY_TX_HINT";
public static final String TERMINOLOGY_TX_WARNING = "TERMINOLOGY_TX_WARNING";
public static final String SD_ED_TYPE_PROFILE_WRONG_TYPE = "SD_ED_TYPE_PROFILE_WRONG_TYPE";
public static final String VALUESET_CONCEPT_DISPLAY_PRESENCE_MIXED = "VALUESET_CONCEPT_DISPLAY_PRESENCE_MIXED";
public static final String VALUESET_CONCEPT_DISPLAY_SCT_TAG_MIXED = "VALUESET_CONCEPT_DISPLAY_SCT_TAG_MIXED";
}

2
org.hl7.fhir.utilities/src/main/resources/Messages.properties
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@ -977,3 +977,5 @@ TERMINOLOGY_TX_HINT = {1}
TERMINOLOGY_TX_WARNING = {1}
SD_ED_TYPE_WRONG_TYPE_one = The element has a type {0} which is different to the type {1} on the base profile {2}
SD_ED_TYPE_WRONG_TYPE_other = The element has a type {0} which is not in the types {1} on the base profile {2}
VALUESET_CONCEPT_DISPLAY_PRESENCE_MIXED = This include has some concepts with displays and some without - check that this is what is intended
VALUESET_CONCEPT_DISPLAY_SCT_TAG_MIXED = 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

95
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ValueSetValidator.java
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@ -22,10 +22,79 @@ import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.validation.instance.type.ValueSetValidator.SystemLevelValidator;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class ValueSetValidator extends BaseValidator {
public class SystemLevelValidator {
protected List<ValidationMessage> errors;
protected Element inc;
protected NodeStack stack;
private boolean noDisplay = false;
private boolean hasDisplay = false;
protected SystemLevelValidator(List<ValidationMessage> errors, Element inc, NodeStack stack) {
super();
this.errors = errors;
this.inc = inc;
this.stack = stack;
}
public void checkConcept(String code, String display) {
if (Utilities.noString(display)) {
noDisplay = true;
} else {
hasDisplay = true;
}
}
public void finish() {
hint(errors, "2023-07-21", IssueType.BUSINESSRULE, inc.line(), inc.col(), stack.getLiteralPath(), !(noDisplay && hasDisplay), I18nConstants.VALUESET_CONCEPT_DISPLAY_PRESENCE_MIXED);
}
}
public class SnomedCTValidator extends SystemLevelValidator {
private boolean noTag = false;
private boolean hasTag = false;
protected SnomedCTValidator(List<ValidationMessage> errors, Element inc, NodeStack stack) {
super(errors, inc, stack);
}
public void checkConcept(String code, String display) {
super.checkConcept(code, display);
if (!Utilities.noString(display)) {
boolean tagged = display.endsWith(")") && display.indexOf("(") > display.length() - 20;
if (tagged) {
hasTag = true;
} else {
noTag = true;
}
}
}
public void finish() {
hint(errors, "2023-07-21", IssueType.BUSINESSRULE, inc.line(), inc.col(), stack.getLiteralPath(), !(noTag && hasTag), I18nConstants.VALUESET_CONCEPT_DISPLAY_SCT_TAG_MIXED);
}
}
public class GeneralValidator extends SystemLevelValidator {
protected GeneralValidator(List<ValidationMessage> errors, Element inc, NodeStack stack) {
super(errors, inc, stack);
}
}
private SystemLevelValidator getSystemValidator(String system, List<ValidationMessage> errors, Element inc, NodeStack stack) {
if (system == null) {
return new GeneralValidator(errors, inc, stack);
}
switch (system) {
case "http://snomed.info/sct" :return new SnomedCTValidator(errors, inc, stack);
default: return new GeneralValidator(errors, inc, stack);
}
}
public class VSCodingValidationRequest extends CodingValidationRequest {
private NodeStack stack;
@ -139,6 +208,8 @@ public class ValueSetValidator extends BaseValidator {
}
List<Element> concepts = include.getChildrenByName("concept");
List<Element> filters = include.getChildrenByName("filter");
SystemLevelValidator slv = getSystemValidator(system, errors, include, stack);
if (!Utilities.noString(system)) {
boolean systemOk = true;
int cc = 0;
@ -147,10 +218,10 @@ public class ValueSetValidator extends BaseValidator {
for (Element concept : concepts) {
// we treat the first differently because we want to know if tbe system is worth validating. if it is, then we batch the rest
if (first) {
systemOk = validateValueSetIncludeConcept(errors, concept, stack, stack.push(concept, cc, null, null), system, version);
systemOk = validateValueSetIncludeConcept(errors, concept, stack, stack.push(concept, cc, null, null), system, version, slv);
first = false;
} else if (systemOk) {
batch.add(prepareValidateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version));
batch.add(prepareValidateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version, slv));
}
cc++;
}
@ -180,19 +251,24 @@ public class ValueSetValidator extends BaseValidator {
int cf = 0;
for (Element filter : filters) {
if (systemOk && !validateValueSetIncludeFilter(errors, include, stack.push(filter, cf, null, null), system, version)) {
if (systemOk && !validateValueSetIncludeFilter(errors, include, stack.push(filter, cf, null, null), system, version, slv)) {
systemOk = false;
}
cf++;
}
slv.finish();
} else {
warning(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stack.getLiteralPath(), filters.size() == 0 && concepts.size() == 0, I18nConstants.VALUESET_NO_SYSTEM_WARNING);
}
return ok;
}
private boolean validateValueSetIncludeConcept(List<ValidationMessage> errors, Element concept, NodeStack stackInc, NodeStack stack, String system, String version) {
private boolean validateValueSetIncludeConcept(List<ValidationMessage> errors, Element concept, NodeStack stackInc, NodeStack stack, String system, String version, SystemLevelValidator slv) {
String code = concept.getChildValue("code");
String display = concept.getChildValue("display");
slv.checkConcept(code, display);
if (version == null) {
ValidationResult vv = context.validateCode(ValidationOptions.defaults(), new Coding(system, code, null), null);
if (vv.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
@ -229,8 +305,11 @@ public class ValueSetValidator extends BaseValidator {
return true;
}
private VSCodingValidationRequest prepareValidateValueSetIncludeConcept(List<ValidationMessage> errors, Element concept, NodeStack stack, String system, String version) {
private VSCodingValidationRequest prepareValidateValueSetIncludeConcept(List<ValidationMessage> errors, Element concept, NodeStack stack, String system, String version, SystemLevelValidator slv) {
String code = concept.getChildValue("code");
String display = concept.getChildValue("display");
slv.checkConcept(code, display);
Coding c = new Coding(system, code, null);
if (version != null) {
c.setVersion(version);
@ -238,7 +317,11 @@ public class ValueSetValidator extends BaseValidator {
return new VSCodingValidationRequest(stack, c);
}
private boolean validateValueSetIncludeFilter(List<ValidationMessage> errors, Element include, NodeStack push, String system, String version) {
private boolean validateValueSetIncludeFilter(List<ValidationMessage> errors, Element filter, NodeStack push, String system, String version, SystemLevelValidator slv) {
//
// String display = concept.getChildValue("display");
// slv.checkConcept(code, display);
return true;
}
}