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Fix NPE handling R3 structure definitions

This commit is contained in:
Grahame Grieve 2023-06-28 05:56:14 +10:00
parent ec8e999162
commit 704d498300
14 changed files with 48 additions and 43 deletions
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2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -2238,7 +2238,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
public List<StructureDefinition> fetchTypeDefinitions(String typeName) {
List<StructureDefinition> res = new ArrayList<>();
structures.listAll(res);
res.removeIf(sd -> !sd.getType().equals(typeName));
res.removeIf(sd -> !sd.hasType() || !sd.getType().equals(typeName));
return res;
}

13
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
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@ -158,15 +158,16 @@ public class BaseValidator implements IValidationContextResourceLoader {
protected Coding jurisdiction;
protected boolean allowExamples;
protected boolean forPublication;
protected boolean debug;
public BaseValidator(IWorkerContext context, XVerExtensionManager xverManager) {
public BaseValidator(IWorkerContext context, XVerExtensionManager xverManager, boolean debug) {
super();
this.context = context;
this.xverManager = xverManager;
if (this.xverManager == null) {
this.xverManager = new XVerExtensionManager(context);
}
this.debug = debug;
}
private boolean doingLevel(IssueSeverity error) {
@ -1272,4 +1273,12 @@ public class BaseValidator implements IValidationContextResourceLoader {
return this;
}
public boolean isDebug() {
return debug;
}
public void setDebug(boolean debug) {
this.debug = debug;
}
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/codesystem/CodeSystemValidator.java
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@ -47,7 +47,7 @@ import org.hl7.fhir.validation.BaseValidator;
public class CodeSystemValidator extends BaseValidator {
public CodeSystemValidator(IWorkerContext context, XVerExtensionManager xverManager) {
super(context, xverManager);
super(context, xverManager, false);
}
public List<ValidationMessage> validate(CodeSystem cs, boolean forBuild) {

33
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -479,7 +479,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
// time tracking
private boolean noBindingMsgSuppressed;
private boolean debug;
private Map<String, Element> fetchCache = new HashMap<>();
private HashMap<Element, ResourceValidationTracker> resourceTracker = new HashMap<>();
private IValidatorResourceFetcher fetcher;
@ -507,7 +506,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private boolean logProgress;
public InstanceValidator(IWorkerContext theContext, IEvaluationContext hostServices, XVerExtensionManager xverManager) {
super(theContext, xverManager);
super(theContext, xverManager, false);
start = System.currentTimeMillis();
this.externalHostServices = hostServices;
this.profileUtilities = new ProfileUtilities(theContext, null, null);
@ -5048,31 +5047,31 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
public boolean checkSpecials(ValidatorHostContext hostContext, List<ValidationMessage> errors, Element element, NodeStack stack, boolean checkSpecials, PercentageTracker pct, ValidationMode mode) {
// specific known special validations
if (element.getType().equals(BUNDLE)) {
return new BundleValidator(context, serverBase, this, xverManager, jurisdiction).validateBundle(errors, element, stack, checkSpecials, hostContext, pct, mode);
return new BundleValidator(context, debug, serverBase, this, xverManager, jurisdiction).validateBundle(errors, element, stack, checkSpecials, hostContext, pct, mode);
} else if (element.getType().equals("Observation")) {
return validateObservation(errors, element, stack);
} else if (element.getType().equals("Questionnaire")) {
return new QuestionnaireValidator(context, myEnableWhenEvaluator, fpe, timeTracker, questionnaireMode, xverManager, jurisdiction).validateQuestionannaire(errors, element, element, stack);
return new QuestionnaireValidator(context, debug, myEnableWhenEvaluator, fpe, timeTracker, questionnaireMode, xverManager, jurisdiction).validateQuestionannaire(errors, element, element, stack);
} else if (element.getType().equals("QuestionnaireResponse")) {
return new QuestionnaireValidator(context, myEnableWhenEvaluator, fpe, timeTracker, questionnaireMode, xverManager, jurisdiction).validateQuestionannaireResponse(hostContext, errors, element, stack);
return new QuestionnaireValidator(context, debug, myEnableWhenEvaluator, fpe, timeTracker, questionnaireMode, xverManager, jurisdiction).validateQuestionannaireResponse(hostContext, errors, element, stack);
} else if (element.getType().equals("Measure")) {
return new MeasureValidator(context, timeTracker, xverManager, jurisdiction, this).validateMeasure(hostContext, errors, element, stack);
return new MeasureValidator(context, debug, timeTracker, xverManager, jurisdiction, this).validateMeasure(hostContext, errors, element, stack);
} else if (element.getType().equals("MeasureReport")) {
return new MeasureValidator(context, timeTracker, xverManager, jurisdiction, this).validateMeasureReport(hostContext, errors, element, stack);
return new MeasureValidator(context, debug, timeTracker, xverManager, jurisdiction, this).validateMeasureReport(hostContext, errors, element, stack);
} else if (element.getType().equals("CapabilityStatement")) {
return validateCapabilityStatement(errors, element, stack);
} else if (element.getType().equals("CodeSystem")) {
return new CodeSystemValidator(context, timeTracker, this, xverManager, jurisdiction).validateCodeSystem(errors, element, stack, baseOptions.withLanguage(stack.getWorkingLang()));
return new CodeSystemValidator(context, debug, timeTracker, this, xverManager, jurisdiction).validateCodeSystem(errors, element, stack, baseOptions.withLanguage(stack.getWorkingLang()));
} else if (element.getType().equals("ConceptMap")) {
return new ConceptMapValidator(context, timeTracker, this, xverManager, jurisdiction).validateConceptMap(errors, element, stack, baseOptions.withLanguage(stack.getWorkingLang()));
return new ConceptMapValidator(context, debug, timeTracker, this, xverManager, jurisdiction).validateConceptMap(errors, element, stack, baseOptions.withLanguage(stack.getWorkingLang()));
} else if (element.getType().equals("SearchParameter")) {
return new SearchParameterValidator(context, timeTracker, fpe, xverManager, jurisdiction).validateSearchParameter(errors, element, stack);
return new SearchParameterValidator(context, debug, timeTracker, fpe, xverManager, jurisdiction).validateSearchParameter(errors, element, stack);
} else if (element.getType().equals("StructureDefinition")) {
return new StructureDefinitionValidator(context, timeTracker, fpe, wantCheckSnapshotUnchanged, xverManager, jurisdiction, forPublication).validateStructureDefinition(errors, element, stack);
return new StructureDefinitionValidator(context, debug, timeTracker, fpe, wantCheckSnapshotUnchanged, xverManager, jurisdiction, forPublication).validateStructureDefinition(errors, element, stack);
} else if (element.getType().equals("StructureMap")) {
return new StructureMapValidator(context, timeTracker, fpe, xverManager,profileUtilities, jurisdiction).validateStructureMap(errors, element, stack);
return new StructureMapValidator(context, debug, timeTracker, fpe, xverManager,profileUtilities, jurisdiction).validateStructureMap(errors, element, stack);
} else if (element.getType().equals("ValueSet")) {
return new ValueSetValidator(context, timeTracker, this, xverManager, jurisdiction, allowExamples).validateValueSet(errors, element, stack);
return new ValueSetValidator(context, debug, timeTracker, this, xverManager, jurisdiction, allowExamples).validateValueSet(errors, element, stack);
} else {
return true;
}
@ -6399,13 +6398,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
public boolean isDebug() {
return debug;
}
public void setDebug(boolean debug) {
this.debug = debug;
}
private String tail(String path) {
return path.substring(path.lastIndexOf(".") + 1);
}

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/BundleValidator.java
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@ -35,8 +35,8 @@ public class BundleValidator extends BaseValidator {
private String serverBase;
private InstanceValidator validator;
public BundleValidator(IWorkerContext context, String serverBase, InstanceValidator validator, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager);
public BundleValidator(IWorkerContext context, boolean debug, String serverBase, InstanceValidator validator, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager, debug);
this.serverBase = serverBase;
this.validator = validator;
this.jurisdiction = jurisdiction;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/CodeSystemValidator.java
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@ -23,8 +23,8 @@ public class CodeSystemValidator extends BaseValidator {
private InstanceValidator parent;
public CodeSystemValidator(IWorkerContext context, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager);
public CodeSystemValidator(IWorkerContext context, boolean debug, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager, debug);
source = Source.InstanceValidator;
this.timeTracker = timeTracker;
this.jurisdiction = jurisdiction;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ConceptMapValidator.java
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@ -54,8 +54,8 @@ public class ConceptMapValidator extends BaseValidator {
private InstanceValidator parent;
public ConceptMapValidator(IWorkerContext context, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager);
public ConceptMapValidator(IWorkerContext context, boolean debug, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager, debug);
source = Source.InstanceValidator;
this.timeTracker = timeTracker;
this.jurisdiction = jurisdiction;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/MeasureValidator.java
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@ -44,8 +44,8 @@ import org.w3c.dom.Document;
public class MeasureValidator extends BaseValidator {
private InstanceValidator parent;
public MeasureValidator(IWorkerContext context, TimeTracker timeTracker, XVerExtensionManager xverManager, Coding jurisdiction, InstanceValidator parent) {
super(context, xverManager);
public MeasureValidator(IWorkerContext context, boolean debug, TimeTracker timeTracker, XVerExtensionManager xverManager, Coding jurisdiction, InstanceValidator parent) {
super(context, xverManager, debug);
source = Source.InstanceValidator;
this.timeTracker = timeTracker;
this.jurisdiction = jurisdiction;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/QuestionnaireValidator.java
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@ -133,8 +133,8 @@ public class QuestionnaireValidator extends BaseValidator {
private FHIRPathEngine fpe;
private QuestionnaireMode questionnaireMode;
public QuestionnaireValidator(IWorkerContext context, EnableWhenEvaluator myEnableWhenEvaluator, FHIRPathEngine fpe, TimeTracker timeTracker, QuestionnaireMode questionnaireMode, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager);
public QuestionnaireValidator(IWorkerContext context, boolean debug, EnableWhenEvaluator myEnableWhenEvaluator, FHIRPathEngine fpe, TimeTracker timeTracker, QuestionnaireMode questionnaireMode, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager, debug);
source = Source.InstanceValidator;
this.myEnableWhenEvaluator = myEnableWhenEvaluator;
this.fpe = fpe;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/SearchParameterValidator.java
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@ -36,8 +36,8 @@ public class SearchParameterValidator extends BaseValidator {
private FHIRPathEngine fpe;
public SearchParameterValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager);
public SearchParameterValidator(IWorkerContext context, boolean debug, TimeTracker timeTracker, FHIRPathEngine fpe, XVerExtensionManager xverManager, Coding jurisdiction) {
super(context, xverManager, debug);
source = Source.InstanceValidator;
this.fpe = fpe;
this.timeTracker = timeTracker;

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
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@ -62,8 +62,8 @@ public class StructureDefinitionValidator extends BaseValidator {
private FHIRPathEngine fpe;
private boolean wantCheckSnapshotUnchanged;
public StructureDefinitionValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe, boolean wantCheckSnapshotUnchanged, XVerExtensionManager xverManager, Coding jurisdiction, boolean forPublication) {
super(context, xverManager);
public StructureDefinitionValidator(IWorkerContext context, boolean debug, TimeTracker timeTracker, FHIRPathEngine fpe, boolean wantCheckSnapshotUnchanged, XVerExtensionManager xverManager, Coding jurisdiction, boolean forPublication) {
super(context, xverManager, debug);
source = Source.InstanceValidator;
this.fpe = fpe;
this.timeTracker = timeTracker;
@ -496,6 +496,9 @@ public class StructureDefinitionValidator extends BaseValidator {
// String upath = profileUrl+"#"+path;
fpe.check(invariant, rootPath, path, fpe.parse(expression));
} catch (Exception e) {
if (debug) {
e.printStackTrace();
}
ok = rule(errors, "2023-06-19", IssueType.INVALID, stack, false, I18nConstants.ED_INVARIANT_EXPRESSION_ERROR, key, expression, e.getMessage()) && ok;
}
}

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureMapValidator.java
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@ -303,8 +303,8 @@ public class StructureMapValidator extends BaseValidator {
private ContextUtilities cu;
private List<StructureMap> imports = new ArrayList<>();
public StructureMapValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe, XVerExtensionManager xverManager, ProfileUtilities profileUtilities, Coding jurisdiction) {
super(context, xverManager);
public StructureMapValidator(IWorkerContext context, boolean debug, TimeTracker timeTracker, FHIRPathEngine fpe, XVerExtensionManager xverManager, ProfileUtilities profileUtilities, Coding jurisdiction) {
super(context, xverManager, debug);
source = Source.InstanceValidator;
this.fpe = fpe;
this.timeTracker = timeTracker;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ValueSetValidator.java
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@ -43,8 +43,8 @@ public class ValueSetValidator extends BaseValidator {
private InstanceValidator parent;
public ValueSetValidator(IWorkerContext context, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction, boolean allowExamples) {
super(context, xverManager);
public ValueSetValidator(IWorkerContext context, boolean debug, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction, boolean allowExamples) {
super(context, xverManager, debug);
source = Source.InstanceValidator;
this.timeTracker = timeTracker;
this.parent = parent;

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/profile/ProfileValidator.java
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@ -55,7 +55,7 @@ public class ProfileValidator extends BaseValidator {
private FHIRPathEngine fpe;
public ProfileValidator(IWorkerContext context, XVerExtensionManager xverManager) {
super(context, xverManager);
super(context, xverManager, false);
fpe = new FHIRPathEngine(context);
fpe.setAllowDoubleQuotes(allowDoubleQuotesInFHIRPath);
}